From 89fb748572ed9b66fc6e0884e7a06cde898755b3 Mon Sep 17 00:00:00 2001
From: Thomas Wiseman <twiseman@wm275-315.lan>
Date: Wed, 18 Jan 2023 15:47:41 -0500
Subject: [PATCH 001/213] workflow trial 1

---
 .github/workflows/travis-to-actions-test.yml | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 .github/workflows/travis-to-actions-test.yml

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
new file mode 100644
index 00000000000..a95dbd1851c
--- /dev/null
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -0,0 +1,17 @@
+name: travis-to-github-test
+run-name: ${{ github.actor }} is testing out workflows. 
+on:
+  push:
+    branches:
+      -travis_to_workflows_test
+
+jobs:
+  check-bats-version:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '14'
+      - run: npm install -g bats
+      - run: bats -v
\ No newline at end of file

From a7f5fe7b3711854492c87d66e60d81bfd010da95 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 15:52:04 -0500
Subject: [PATCH 002/213] udate

---
 .github/workflows/travis-to-actions-test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index a95dbd1851c..f1f6f497995 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -1,9 +1,10 @@
 name: travis-to-github-test
 run-name: ${{ github.actor }} is testing out workflows. 
 on:
+  workflow_dispatch:
   push:
     branches:
-      -travis_to_workflows_test
+      - travis_to_workflows_test
 
 jobs:
   check-bats-version:

From c619a6132aec5391b224f5807887e9a9ca4afc8c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 15:56:50 -0500
Subject: [PATCH 003/213] remove trigger

---
 .github/workflows/travis-to-actions-test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index f1f6f497995..295cc3e3cdd 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -1,7 +1,6 @@
 name: travis-to-github-test
 run-name: ${{ github.actor }} is testing out workflows. 
 on:
-  workflow_dispatch:
   push:
     branches:
       - travis_to_workflows_test

From 900da1b464de11ed91df6caaba1bbbbf010b36ec Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:15:28 -0500
Subject: [PATCH 004/213] add workflow_dispatch

---
 .github/workflows/travis-to-actions-test.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 295cc3e3cdd..cbf5ecee1f3 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -1,6 +1,12 @@
 name: travis-to-github-test
-run-name: ${{ github.actor }} is testing out workflows. 
+
+#This is what shows up in the github workflows page as the title. 
+run-name: ${{ github.actor }} is testing out workflows.
+
+#What triggers the workflow to run.
+#Currently limited to git push on the travis branch. 
 on:
+  workflow_dispatcb:
   push:
     branches:
       - travis_to_workflows_test

From 41b4fc58f048a983a5332fd3bb917e1620e5565c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:16:42 -0500
Subject: [PATCH 005/213] fix spelling mistake

---
 .github/workflows/travis-to-actions-test.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index cbf5ecee1f3..6cd5145f22b 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -4,10 +4,9 @@ name: travis-to-github-test
 run-name: ${{ github.actor }} is testing out workflows.
 
 #What triggers the workflow to run.
-#Currently limited to git push on the travis branch. 
 on:
-  workflow_dispatcb:
-  push:
+  workflow_dispatch: #Manual trigger from GitHub UI
+  push: #On push to specified branches. 
     branches:
       - travis_to_workflows_test
 

From b742a6b1d304859fe31d0143aa3ac83838a86891 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:22:26 -0500
Subject: [PATCH 006/213] echo environment variables

---
 .github/workflows/travis-to-actions-test.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 6cd5145f22b..447fe1db760 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -10,6 +10,10 @@ on:
     branches:
       - travis_to_workflows_test
 
+env:
+  BUILD_TYPE: centaurAws
+  BUILD_MYSQL: 5.7
+
 jobs:
   check-bats-version:
     runs-on: ubuntu-latest
@@ -19,4 +23,5 @@ jobs:
         with:
           node-version: '14'
       - run: npm install -g bats
-      - run: bats -v
\ No newline at end of file
+      - run: bats -v
+      - run: echo "Build Type: $BUILD_TYPE\n Build MySQL: $BUILD_MYSQL"
\ No newline at end of file

From 2c8fe9405b5f876b240939ad607d145f8e0a9ffa Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:25:04 -0500
Subject: [PATCH 007/213] typo

---
 .github/workflows/travis-to-actions-test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 447fe1db760..600682c0910 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -24,4 +24,5 @@ jobs:
           node-version: '14'
       - run: npm install -g bats
       - run: bats -v
-      - run: echo "Build Type: $BUILD_TYPE\n Build MySQL: $BUILD_MYSQL"
\ No newline at end of file
+      - run: echo "Build Type $BUILD_TYPE"
+      - run: echo "Build MySQL $BUILD_MYSQL"
\ No newline at end of file

From ef5540f13a5cede8187c88612c267239fbe40595 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:28:04 -0500
Subject: [PATCH 008/213] change enviornment variable scope

---
 .github/workflows/travis-to-actions-test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 600682c0910..2ad0e583a51 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -10,12 +10,12 @@ on:
     branches:
       - travis_to_workflows_test
 
-env:
-  BUILD_TYPE: centaurAws
-  BUILD_MYSQL: 5.7
 
 jobs:
   check-bats-version:
+    env:
+      BUILD_TYPE: centaurAws
+      BUILD_MYSQL: 5.7
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3

From 3960e6aad493678174411cfde7147f9f65d857b4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:29:55 -0500
Subject: [PATCH 009/213] it was working the first time

---
 .github/workflows/travis-to-actions-test.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 2ad0e583a51..061ea97fb9b 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -10,12 +10,13 @@ on:
     branches:
       - travis_to_workflows_test
 
+#Global environment variables.
+env:
+  BUILD_TYPE: centaurAws
+  BUILD_MYSQL: 5.7
 
 jobs:
   check-bats-version:
-    env:
-      BUILD_TYPE: centaurAws
-      BUILD_MYSQL: 5.7
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3

From 047b9572992c5bdccd2ab99ff1f498c97bf98383 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:39:43 -0500
Subject: [PATCH 010/213] here goes nothing

---
 .github/workflows/travis-to-actions-test.yml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 061ea97fb9b..805d93b3286 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -1,4 +1,5 @@
-name: travis-to-github-test
+name: 'Build Cromwell Test'
+
 
 #This is what shows up in the github workflows page as the title. 
 run-name: ${{ github.actor }} is testing out workflows.
@@ -10,13 +11,16 @@ on:
     branches:
       - travis_to_workflows_test
 
+permissions: 
+  contents: read
+
 #Global environment variables.
 env:
   BUILD_TYPE: centaurAws
   BUILD_MYSQL: 5.7
 
 jobs:
-  check-bats-version:
+  check-bats-version: #Sanity check not related to Cromwell. Should always pass. 
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
@@ -26,4 +30,9 @@ jobs:
       - run: npm install -g bats
       - run: bats -v
       - run: echo "Build Type $BUILD_TYPE"
-      - run: echo "Build MySQL $BUILD_MYSQL"
\ No newline at end of file
+      - run: echo "Build MySQL $BUILD_MYSQL"
+  run-shell-script:
+    runs-on: ubuntu-latest
+    steps:
+      - run: src/ci/bin/test.sh
+  
\ No newline at end of file

From f8f73c72ef3ad883ba2cd73cb14b44815a2c3cdb Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:41:37 -0500
Subject: [PATCH 011/213] getting my bearings

---
 .github/workflows/travis-to-actions-test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 805d93b3286..69d8f767732 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -34,5 +34,7 @@ jobs:
   run-shell-script:
     runs-on: ubuntu-latest
     steps:
+      - run: pwd
+      - run: bash -c 'echo $BASH_VERSION'
       - run: src/ci/bin/test.sh
   
\ No newline at end of file

From 85e949e7390b69ad197cdecb7256642afd8c9991 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:42:40 -0500
Subject: [PATCH 012/213] dotslash

---
 .github/workflows/travis-to-actions-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 69d8f767732..f7f5490e134 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -36,5 +36,5 @@ jobs:
     steps:
       - run: pwd
       - run: bash -c 'echo $BASH_VERSION'
-      - run: src/ci/bin/test.sh
+      - run: ./src/ci/bin/test.sh
   
\ No newline at end of file

From a0285509ce65cbcb043e3204d8f4910e2b4a203a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:44:28 -0500
Subject: [PATCH 013/213] are you suuuuure git?

---
 .github/workflows/travis-to-actions-test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index f7f5490e134..d1faad12b41 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -35,6 +35,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - run: pwd
+      - run: ls
       - run: bash -c 'echo $BASH_VERSION'
       - run: ./src/ci/bin/test.sh
   
\ No newline at end of file

From 92075529b0fc349a8bd3db5da027b97ebc72513d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:47:05 -0500
Subject: [PATCH 014/213] checkout first

---
 .github/workflows/travis-to-actions-test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index d1faad12b41..0464838f03c 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -34,6 +34,10 @@ jobs:
   run-shell-script:
     runs-on: ubuntu-latest
     steps:
+      -
+      name: Checkout
+      uses: actions/checkout@v3
+      -
       - run: pwd
       - run: ls
       - run: bash -c 'echo $BASH_VERSION'

From 49c45bf93f511f873982d89cf8906c4c9c764d22 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:49:20 -0500
Subject: [PATCH 015/213] formatting

---
 .github/workflows/travis-to-actions-test.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 0464838f03c..b6c9b5136ac 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -34,10 +34,8 @@ jobs:
   run-shell-script:
     runs-on: ubuntu-latest
     steps:
-      -
-      name: Checkout
-      uses: actions/checkout@v3
-      -
+      - name: Checkout
+      - uses: actions/checkout@v3
       - run: pwd
       - run: ls
       - run: bash -c 'echo $BASH_VERSION'

From 2daf2d6f82218e94520a5d33c945fb0b0e9822d1 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 12:52:47 -0500
Subject: [PATCH 016/213] try this

---
 .github/workflows/travis-to-actions-test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index b6c9b5136ac..97169419ceb 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -35,9 +35,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-      - uses: actions/checkout@v3
-      - run: pwd
-      - run: ls
-      - run: bash -c 'echo $BASH_VERSION'
-      - run: ./src/ci/bin/test.sh
+        uses: actions/checkout@v3
+        run: pwd
+        run: ls
+        run: bash -c 'echo $BASH_VERSION'
+        run: ./src/ci/bin/test.sh
   
\ No newline at end of file

From 6fc8470607e7a86d8597a3e721159e40034de372 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 13:08:53 -0500
Subject: [PATCH 017/213] steal from adam

---
 .github/workflows/travis-to-actions-test.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 97169419ceb..6a9b3d13e68 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -31,13 +31,14 @@ jobs:
       - run: bats -v
       - run: echo "Build Type $BUILD_TYPE"
       - run: echo "Build MySQL $BUILD_MYSQL"
-  run-shell-script:
-    runs-on: ubuntu-latest
+  build-and-test:
+    name: SBT unit tests
+    runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-        run: pwd
-        run: ls
-        run: bash -c 'echo $BASH_VERSION'
-        run: ./src/ci/bin/test.sh
+    - name: Clone Cromwell
+      uses: actions/checkout@v2
+      with:
+        repository: broadinstitute/cromwell
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
+        path: cromwell
   
\ No newline at end of file

From 776e4a91983bdf9e69b98a5528af05629208fa4e Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 13:11:08 -0500
Subject: [PATCH 018/213] with scala

---
 .github/workflows/travis-to-actions-test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 6a9b3d13e68..0bab2646c2e 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -41,4 +41,7 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
+    - uses: olafurpg/setup-scala@v10
+      with:
+        java-version: adopt@1.11
   
\ No newline at end of file

From 426044ae8ed534c9fdc48c7d9e5946e248d7dab4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 23 Jan 2023 13:13:49 -0500
Subject: [PATCH 019/213] full steal

---
 .github/workflows/travis-to-actions-test.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 0bab2646c2e..3e92dc33803 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -44,4 +44,12 @@ jobs:
     - uses: olafurpg/setup-scala@v10
       with:
         java-version: adopt@1.11
-  
\ No newline at end of file
+    - name: Run tests
+      run: |
+        set -e
+        cd cromwell
+        sbt \
+          -Dsbt.supershell=false \
+          -Dakka.test.timefactor=10 \
+          -Dbackend.providers.Local.config.filesystems.local.localization.0=copy \
+          test
\ No newline at end of file

From 6b30ef42b3aee43c1ab454d4fbcdc7335bb6faf7 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 24 Jan 2023 13:23:19 -0500
Subject: [PATCH 020/213] v3 newer than v2

---
 .github/workflows/travis-to-actions-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 3e92dc33803..c8672a587ba 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -36,7 +36,7 @@ jobs:
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     steps:
     - name: Clone Cromwell
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work

From 61704c812312ab43cf366f76c87090836d346fbc Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 24 Jan 2023 15:27:14 -0500
Subject: [PATCH 021/213] moment of truth

---
 .github/workflows/travis-to-actions-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index c8672a587ba..5855bbc12cb 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -52,4 +52,4 @@ jobs:
           -Dsbt.supershell=false \
           -Dakka.test.timefactor=10 \
           -Dbackend.providers.Local.config.filesystems.local.localization.0=copy \
-          test
\ No newline at end of file
+          testOnly common.util.VersionUtilSpec
\ No newline at end of file

From 4c70191c647fddfcdc4e6e1cc61dafcf297b49fd Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 24 Jan 2023 15:41:40 -0500
Subject: [PATCH 022/213] will this work?

---
 .github/workflows/travis-to-actions-test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 5855bbc12cb..39c545d1e44 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -51,5 +51,5 @@ jobs:
         sbt \
           -Dsbt.supershell=false \
           -Dakka.test.timefactor=10 \
-          -Dbackend.providers.Local.config.filesystems.local.localization.0=copy \
-          testOnly common.util.VersionUtilSpec
\ No newline at end of file
+          -Dbackend.providers.Local.config.filesystems.local.localization.0=copy
+        testOnly common.util.VersionUtilSpec
\ No newline at end of file

From da89730bacb72248c1f4debd7477c094311f3ac3 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 24 Jan 2023 16:14:11 -0500
Subject: [PATCH 023/213] this is the secret sauce

---
 .github/workflows/travis-to-actions-test.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 39c545d1e44..076e4191026 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -48,8 +48,4 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt \
-          -Dsbt.supershell=false \
-          -Dakka.test.timefactor=10 \
-          -Dbackend.providers.Local.config.filesystems.local.localization.0=copy
-        testOnly common.util.VersionUtilSpec
\ No newline at end of file
+        sbt "test:testOnly common.util.VersionUtilSpec"
\ No newline at end of file

From 6c623ed9b0e08af4cc57900f7d3cc78d4a32322f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 12:48:14 -0500
Subject: [PATCH 024/213] This should still be working

---
 .github/workflows/travis-to-actions-test.yml | 23 +++++---------------
 1 file changed, 5 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 076e4191026..63308507107 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -1,15 +1,13 @@
-name: 'Build Cromwell Test'
-
+name: 'Basic Unit Test'
 
 #This is what shows up in the github workflows page as the title. 
-run-name: ${{ github.actor }} is testing out workflows.
+run-name: ${{ github.actor }} running Basic Unit Test.
 
 #What triggers the workflow to run.
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
-  push: #On push to specified branches. 
-    branches:
-      - travis_to_workflows_test
+  push:
+  pull_request: 
 
 permissions: 
   contents: read
@@ -20,19 +18,8 @@ env:
   BUILD_MYSQL: 5.7
 
 jobs:
-  check-bats-version: #Sanity check not related to Cromwell. Should always pass. 
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '14'
-      - run: npm install -g bats
-      - run: bats -v
-      - run: echo "Build Type $BUILD_TYPE"
-      - run: echo "Build MySQL $BUILD_MYSQL"
   build-and-test:
-    name: SBT unit tests
+    name: SBT VersionUtilSpec test
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     steps:
     - name: Clone Cromwell

From e6cd8756c70b4216c2dd9b4b9132a1df4f641e6a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 12:58:46 -0500
Subject: [PATCH 025/213] one more test

---
 .github/workflows/travis-to-actions-test.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index 63308507107..da21de478a3 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -1,5 +1,7 @@
 name: 'Basic Unit Test'
 
+#The goal of this Github Action is to verify that 
+
 #This is what shows up in the github workflows page as the title. 
 run-name: ${{ github.actor }} running Basic Unit Test.
 
@@ -14,12 +16,12 @@ permissions:
 
 #Global environment variables.
 env:
-  BUILD_TYPE: centaurAws
-  BUILD_MYSQL: 5.7
+  #BUILD_TYPE: centaurAws
+  #BUILD_MYSQL: 5.7
 
 jobs:
   build-and-test:
-    name: SBT VersionUtilSpec test
+    name: SBT VersionUtilSpec testgig
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     steps:
     - name: Clone Cromwell
@@ -28,7 +30,7 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: olafurpg/setup-scala@v10
+    - uses: olafurpg/setup-scala@v11
       with:
         java-version: adopt@1.11
     - name: Run tests

From 23b5f539854ec7b744a44b54b1e4e71959272960 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 13:03:16 -0500
Subject: [PATCH 026/213] try again

---
 .github/workflows/travis-to-actions-test.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index da21de478a3..c1ca0cfb3cd 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -14,11 +14,6 @@ on:
 permissions: 
   contents: read
 
-#Global environment variables.
-env:
-  #BUILD_TYPE: centaurAws
-  #BUILD_MYSQL: 5.7
-
 jobs:
   build-and-test:
     name: SBT VersionUtilSpec testgig
@@ -33,7 +28,7 @@ jobs:
     - uses: olafurpg/setup-scala@v11
       with:
         java-version: adopt@1.11
-    - name: Run tests
+    - name: Run tests #Invoke SBT with an argument asking it to run a specific test.
       run: |
         set -e
         cd cromwell

From 079b3c62cc5cfea9f9bb8874fa7c0255efbec284 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 13:12:17 -0500
Subject: [PATCH 027/213] spelling

---
 .github/workflows/travis-to-actions-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/travis-to-actions-test.yml
index c1ca0cfb3cd..1649630edbb 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/travis-to-actions-test.yml
@@ -16,7 +16,7 @@ permissions:
 
 jobs:
   build-and-test:
-    name: SBT VersionUtilSpec testgig
+    name: SBT VersionUtilSpec Unit Test
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     steps:
     - name: Clone Cromwell

From b435c7add8e5ca06d215ccf1ad45dd5557526f76 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 13:20:07 -0500
Subject: [PATCH 028/213] rename file

---
 .../{travis-to-actions-test.yml => basic_unit_test.yml}         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename .github/workflows/{travis-to-actions-test.yml => basic_unit_test.yml} (89%)

diff --git a/.github/workflows/travis-to-actions-test.yml b/.github/workflows/basic_unit_test.yml
similarity index 89%
rename from .github/workflows/travis-to-actions-test.yml
rename to .github/workflows/basic_unit_test.yml
index 1649630edbb..822121339ae 100644
--- a/.github/workflows/travis-to-actions-test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -23,7 +23,7 @@ jobs:
       uses: actions/checkout@v3
       with:
         repository: broadinstitute/cromwell
-        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
         path: cromwell
     - uses: olafurpg/setup-scala@v11
       with:

From d1e7629b69b42573a49dddabb0fb8204e02f3424 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 13:25:31 -0500
Subject: [PATCH 029/213] comments

---
 .github/workflows/basic_unit_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 822121339ae..71a192e6f97 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -1,11 +1,11 @@
 name: 'Basic Unit Test'
 
-#The goal of this Github Action is to verify that 
+#The goal of this Github Action is to verify that is is possible to compile cromwell (enough) to run a simple unit test.
 
 #This is what shows up in the github workflows page as the title. 
 run-name: ${{ github.actor }} running Basic Unit Test.
 
-#What triggers the workflow to run.
+#What will trigger the workflow to run. 
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
   push:

From 2da9d834f663df28fb6bf58960a41ad9f5c0c717 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 13:31:41 -0500
Subject: [PATCH 030/213] optimize command

---
 .github/workflows/basic_unit_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 71a192e6f97..e04a69f50c9 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -28,8 +28,8 @@ jobs:
     - uses: olafurpg/setup-scala@v11
       with:
         java-version: adopt@1.11
-    - name: Run tests #Invoke SBT with an argument asking it to run a specific test.
+    - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
       run: |
         set -e
         cd cromwell
-        sbt "test:testOnly common.util.VersionUtilSpec"
\ No newline at end of file
+        sbt "common/testOnly common.util.VersionUtilSpec"
\ No newline at end of file

From 9d12de0650bd87d4dd17e501c254701148236149 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:28:19 -0500
Subject: [PATCH 031/213] test with matrix

---
 .github/workflows/basic_unit_test.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index e04a69f50c9..fb39cd1d2be 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -18,6 +18,9 @@ jobs:
   build-and-test:
     name: SBT VersionUtilSpec Unit Test
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
+    strategy:
+    matrix:
+      project: [common, wom, engine]
     steps:
     - name: Clone Cromwell
       uses: actions/checkout@v3
@@ -32,4 +35,4 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt "common/testOnly common.util.VersionUtilSpec"
\ No newline at end of file
+        sbt "${{ matrix.project }}/testOnly common.util.VersionUtilSpec"
\ No newline at end of file

From 076ed6a308e961fe2e97586afd16bcb5c14e1379 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:30:12 -0500
Subject: [PATCH 032/213] try something else

---
 .github/workflows/basic_unit_test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index fb39cd1d2be..cbaa0f1bbba 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -18,7 +18,6 @@ jobs:
   build-and-test:
     name: SBT VersionUtilSpec Unit Test
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
-    strategy:
     matrix:
       project: [common, wom, engine]
     steps:
@@ -35,4 +34,4 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt "${{ matrix.project }}/testOnly common.util.VersionUtilSpec"
\ No newline at end of file
+        sbt "${{ matrix.project }}/testOnly common.util.VersionUtilSpec"g
\ No newline at end of file

From 75c0955542ef4bf1691e88fa85b8f76b73fddef4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:33:26 -0500
Subject: [PATCH 033/213] tab

---
 .github/workflows/basic_unit_test.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index cbaa0f1bbba..f6505474c1a 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -18,8 +18,9 @@ jobs:
   build-and-test:
     name: SBT VersionUtilSpec Unit Test
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
-    matrix:
-      project: [common, wom, engine]
+    strategy:
+      matrix:
+        project: [common, wom, engine]
     steps:
     - name: Clone Cromwell
       uses: actions/checkout@v3

From efbc02c1a67e0ceae2e653a6d166bc659e087c12 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:37:03 -0500
Subject: [PATCH 034/213] more realistic workflow

---
 .github/workflows/basic_unit_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index f6505474c1a..eaeef3d554b 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -35,4 +35,4 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt "${{ matrix.project }}/testOnly common.util.VersionUtilSpec"g
\ No newline at end of file
+        sbt "${{ matrix.project }}/test"
\ No newline at end of file

From 8bb541c442fd08f5b16f75ee09b73e13b0a380c6 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:42:25 -0500
Subject: [PATCH 035/213] why fail fast if you can prolong your failure

---
 .github/workflows/basic_unit_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index eaeef3d554b..b46cff10264 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -20,6 +20,7 @@ jobs:
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     strategy:
       matrix:
+        fail-fast: false
         project: [common, wom, engine]
     steps:
     - name: Clone Cromwell

From 347679658d4373749336cc8509a0b98bf70d831d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:45:03 -0500
Subject: [PATCH 036/213] continue on error

---
 .github/workflows/basic_unit_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index b46cff10264..46c731baf66 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -20,7 +20,7 @@ jobs:
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     strategy:
       matrix:
-        fail-fast: false
+        continue-on-error: true
         project: [common, wom, engine]
     steps:
     - name: Clone Cromwell

From 6b8afdbd5a1d63f3db6d4e72a974f4d5264c9d34 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 25 Jan 2023 15:47:35 -0500
Subject: [PATCH 037/213] syntax

---
 .github/workflows/basic_unit_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 46c731baf66..9258fd71bbf 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -19,8 +19,8 @@ jobs:
     name: SBT VersionUtilSpec Unit Test
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     strategy:
+      fail-fast: false
       matrix:
-        continue-on-error: true
         project: [common, wom, engine]
     steps:
     - name: Clone Cromwell

From e9018d8fe4fe04071a3cb3efa8ce99cc7a568300 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 14:33:01 -0500
Subject: [PATCH 038/213] updated yaml

---
 .github/workflows/basic_unit_test.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 9258fd71bbf..f9de9922557 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -17,23 +17,24 @@ permissions:
 jobs:
   build-and-test:
     name: SBT VersionUtilSpec Unit Test
-    runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
-    strategy:
-      fail-fast: false
-      matrix:
-        project: [common, wom, engine]
+    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have SBT installed by default.
     steps:
+    - uses: actions/checkout@v3
+    - uses: coursier/cache-action@v6
     - name: Clone Cromwell
       uses: actions/checkout@v3
       with:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
         path: cromwell
-    - uses: olafurpg/setup-scala@v11
+    - name: Setup JDK
+      uses: actions/setup-java@v3
       with:
-        java-version: adopt@1.11
+        distribution: temurin
+        java-version: 11
+        cache: sbt
     - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
       run: |
         set -e
         cd cromwell
-        sbt "${{ matrix.project }}/test"
\ No newline at end of file
+        sbt "common/testOnly common.util.VersionUtilSpec"
\ No newline at end of file

From f6cce2fc8c5f6f4a480ef596e72cb5b4dd18a790 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 14:35:12 -0500
Subject: [PATCH 039/213] git secrets attempt

---
 .github/workflows/basic_unit_test.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index f9de9922557..4569d2ff7a3 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -21,6 +21,17 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - uses: coursier/cache-action@v6
+    - name: Git secrets setup
+      run: |
+        git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+        cd ~/git-secrets
+        git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
+        sudo make install
+    - name: Secrets check
+      run: |
+        sudo ln -s "$(which echo)" /usr/local/bin/say
+        ./minnie-kenny.sh --force
+        git secrets --scan-history
     - name: Clone Cromwell
       uses: actions/checkout@v3
       with:

From b727570b08d3b70ed3f0b09eb4d338fa99abec34 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 14:38:09 -0500
Subject: [PATCH 040/213] bigger test suite

---
 .github/workflows/basic_unit_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 4569d2ff7a3..e20f43287ba 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -48,4 +48,4 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt "common/testOnly common.util.VersionUtilSpec"
\ No newline at end of file
+        sbt "common/test"
\ No newline at end of file

From a399d1267c5d0a526285c453c725c88eb1c05827 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 14:48:51 -0500
Subject: [PATCH 041/213] path stuff

---
 .github/workflows/basic_unit_test.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index e20f43287ba..a74b1d34629 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -37,7 +37,6 @@ jobs:
       with:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
-        path: cromwell
     - name: Setup JDK
       uses: actions/setup-java@v3
       with:
@@ -47,5 +46,4 @@ jobs:
     - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
       run: |
         set -e
-        cd cromwell
         sbt "common/test"
\ No newline at end of file

From c36fd9140017707a5c31f2a720043b1cd63b517d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 14:51:41 -0500
Subject: [PATCH 042/213] yolo

---
 .github/workflows/basic_unit_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index a74b1d34629..4369687bef8 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -46,4 +46,4 @@ jobs:
     - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
       run: |
         set -e
-        sbt "common/test"
\ No newline at end of file
+        sbt "test"
\ No newline at end of file

From 0349d6d758c419b29b88539450c6ea12d97546b7 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 15:42:09 -0500
Subject: [PATCH 043/213] name cache setup

---
 .github/workflows/basic_unit_test.yml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 4369687bef8..7e283fe7e45 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -17,11 +17,13 @@ permissions:
 jobs:
   build-and-test:
     name: SBT VersionUtilSpec Unit Test
-    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have SBT installed by default.
+    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     steps:
-    - uses: actions/checkout@v3
-    - uses: coursier/cache-action@v6
-    - name: Git secrets setup
+    - name: Coursier Cache Setup #Allow sbt to cache setup stuff between github acitons
+      uses: actions/checkout@v3
+      uses: coursier/cache-action@v6  
+
+    - name: Git secrets setup #The Broad requires git-secrets be setup. The Secrets check below veritfies that the setup worked.
       run: |
         git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
         cd ~/git-secrets
@@ -32,6 +34,7 @@ jobs:
         sudo ln -s "$(which echo)" /usr/local/bin/say
         ./minnie-kenny.sh --force
         git secrets --scan-history
+
     - name: Clone Cromwell
       uses: actions/checkout@v3
       with:
@@ -46,4 +49,4 @@ jobs:
     - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
       run: |
         set -e
-        sbt "test"
\ No newline at end of file
+        sbt "services/testOnly *WriteMetadataActorSpec"
\ No newline at end of file

From d84cbabe14cfcb9ab6ee39faeb98354ae8329d2c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 15:43:38 -0500
Subject: [PATCH 044/213] hyphens

---
 .github/workflows/basic_unit_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 7e283fe7e45..638b4ef4b9b 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -20,8 +20,8 @@ jobs:
     runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     steps:
     - name: Coursier Cache Setup #Allow sbt to cache setup stuff between github acitons
-      uses: actions/checkout@v3
-      uses: coursier/cache-action@v6  
+    - uses: actions/checkout@v3
+    - uses: coursier/cache-action@v6  
 
     - name: Git secrets setup #The Broad requires git-secrets be setup. The Secrets check below veritfies that the setup worked.
       run: |

From aee9df5877dd2339b516532325937f9653376532 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 15:49:06 -0500
Subject: [PATCH 045/213] steps

---
 .github/workflows/basic_unit_test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 638b4ef4b9b..331ddf28f21 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -19,9 +19,10 @@ jobs:
     name: SBT VersionUtilSpec Unit Test
     runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     steps:
-    - name: Coursier Cache Setup #Allow sbt to cache setup stuff between github acitons
     - uses: actions/checkout@v3
+      name: Checkout Coursier Cache
     - uses: coursier/cache-action@v6  
+      name: Enable Coursier Cache
 
     - name: Git secrets setup #The Broad requires git-secrets be setup. The Secrets check below veritfies that the setup worked.
       run: |

From aaeee6f5eb17f38e3b2f27fb18a2c9d748b606ce Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 15:55:49 -0500
Subject: [PATCH 046/213] do we even need that?

---
 .github/workflows/basic_unit_test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 331ddf28f21..fb664b5110f 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -37,7 +37,6 @@ jobs:
         git secrets --scan-history
 
     - name: Clone Cromwell
-      uses: actions/checkout@v3
       with:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}

From adcfae889319e18f84e04aa01003301419fa4447 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 15:57:43 -0500
Subject: [PATCH 047/213] yes we need that

---
 .github/workflows/basic_unit_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index fb664b5110f..331ddf28f21 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -37,6 +37,7 @@ jobs:
         git secrets --scan-history
 
     - name: Clone Cromwell
+      uses: actions/checkout@v3
       with:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}

From eda3f89cf9abe9b33eac06a5e19bc2f233e7d985 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 16:01:57 -0500
Subject: [PATCH 048/213] please don't break the internet

---
 .github/workflows/basic_unit_test.yml | 55 ++++++++++++++++++++++++++-
 1 file changed, 53 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 331ddf28f21..dcbd5bfc95e 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -16,7 +16,58 @@ permissions:
 
 jobs:
   build-and-test:
-    name: SBT VersionUtilSpec Unit Test
+    strategy:
+    matrix:
+      sbtSubProject: 
+        [awsBackend,
+        awsS3FileSystem,
+        azureBlobFileSystem,
+        backend,
+        centaur,
+        cloud-nio-impl-drs,
+        cloud-nio-impl-ftp,
+        cloud-nio-spi,
+        Cloud-nio-util,
+        cloudSupport,
+        common,
+        core,
+        cromiam,
+        cromwell-drs-localizer,
+        cromwellApiClient,
+        databaseMigration,
+        databaseSql,
+        dockerHashing,
+        drsFileSystem,
+        engine,
+        ftpFileSystem,
+        gcsFileSystem,
+        googlePipelinesCommon,
+        googlePipelinesV2Alpha1,
+        googlePipelinesV2Beta,
+        httpFileSystem,
+        languageFactoryCore,
+        perf,
+        server,
+        services,
+        sfsBackend,
+        sraFileSystem,
+        tesBackend,
+        wdlBiscayneLanguageFactory,
+        wdlDraft2LanguageFactory,
+        wdlDraft3LanguageFactory,
+        wdlModelBiscayne,
+        wdlModelDraft2,
+        wdlModelDraft3,
+        wdlNewBaseTransforms,
+        wdlSharedModel,
+        wdlSharedTransforms,
+        wdlTransformsBiscayne,
+        wdlTransformsDraft2,
+        wdlTransformsDraft3,
+        wes2cromwell,
+        wom,
+        womtool]
+    name: ${{ matrix.sbtSubProject }} Unit Tests
     runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     steps:
     - uses: actions/checkout@v3
@@ -50,4 +101,4 @@ jobs:
     - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
       run: |
         set -e
-        sbt "services/testOnly *WriteMetadataActorSpec"
\ No newline at end of file
+        sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file

From 81ce1da31e5fcb75ee13a5b718629701f25bd8bd Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 16:04:09 -0500
Subject: [PATCH 049/213] syntax error this

---
 .github/workflows/basic_unit_test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index dcbd5bfc95e..e0be075181c 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -18,8 +18,7 @@ jobs:
   build-and-test:
     strategy:
     matrix:
-      sbtSubProject: 
-        [awsBackend,
+      sbtSubProject: [awsBackend,
         awsS3FileSystem,
         azureBlobFileSystem,
         backend,

From a985a646b52336b3bc6b05986ac8a60b3c77d064 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 16:09:59 -0500
Subject: [PATCH 050/213] desparate

---
 .github/workflows/basic_unit_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index e0be075181c..5dccfadafd3 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -16,6 +16,7 @@ permissions:
 
 jobs:
   build-and-test:
+    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     strategy:
     matrix:
       sbtSubProject: [awsBackend,
@@ -66,8 +67,7 @@ jobs:
         wes2cromwell,
         wom,
         womtool]
-    name: ${{ matrix.sbtSubProject }} Unit Tests
-    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
+    #name: ${{ matrix.sbtSubProject }} Unit Tests
     steps:
     - uses: actions/checkout@v3
       name: Checkout Coursier Cache

From d4da61f28b7f3cfe71e6d0e57d55e26014e2fc28 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 16:12:54 -0500
Subject: [PATCH 051/213] no more

---
 .github/workflows/basic_unit_test.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 5dccfadafd3..1506e26fca0 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -16,10 +16,10 @@ permissions:
 
 jobs:
   build-and-test:
-    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     strategy:
-    matrix:
-      sbtSubProject: [awsBackend,
+      fail-fast: false  
+      matrix:
+        sbtSubProject: [awsBackend,
         awsS3FileSystem,
         azureBlobFileSystem,
         backend,
@@ -67,6 +67,7 @@ jobs:
         wes2cromwell,
         wom,
         womtool]
+    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     #name: ${{ matrix.sbtSubProject }} Unit Tests
     steps:
     - uses: actions/checkout@v3

From 3132a19dc52d62fe60624b1d912258a96f98a8b6 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 16:18:11 -0500
Subject: [PATCH 052/213] case sensitive and so am I

---
 .github/workflows/basic_unit_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 1506e26fca0..65ce396069c 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -27,7 +27,7 @@ jobs:
         cloud-nio-impl-drs,
         cloud-nio-impl-ftp,
         cloud-nio-spi,
-        Cloud-nio-util,
+        cloud-nio-util,
         cloudSupport,
         common,
         core,

From ae82349b55d77b0b1e3e9e5aad2a5b8f717ad3a8 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 16:31:04 -0500
Subject: [PATCH 053/213] commentos

---
 .github/workflows/basic_unit_test.yml | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/basic_unit_test.yml
index 65ce396069c..4bde51e6db9 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/basic_unit_test.yml
@@ -1,9 +1,10 @@
 name: 'Basic Unit Test'
 
-#The goal of this Github Action is to verify that is is possible to compile cromwell (enough) to run a simple unit test.
+#This github action runs all of Cromwell's unit tests.
+#A matrix strategy is used so that each subproject can be unit tested in parallel with all other subprojects. 
 
 #This is what shows up in the github workflows page as the title. 
-run-name: ${{ github.actor }} running Basic Unit Test.
+run-name: ${{ github.actor }} running Cromwell sbt Unit Tests.
 
 #What will trigger the workflow to run. 
 on:
@@ -15,10 +16,10 @@ permissions:
   contents: read
 
 jobs:
-  build-and-test:
+  build-and-test: #This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
     strategy:
-      fail-fast: false  
-      matrix:
+      fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
+      matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
         sbtSubProject: [awsBackend,
         awsS3FileSystem,
         azureBlobFileSystem,
@@ -67,15 +68,19 @@ jobs:
         wes2cromwell,
         wom,
         womtool]
+
     runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
-    #name: ${{ matrix.sbtSubProject }} Unit Tests
+
     steps:
+
+    #Allows this github action to use a cache to store stuff like Java and SBT files between runs.
     - uses: actions/checkout@v3
       name: Checkout Coursier Cache
     - uses: coursier/cache-action@v6  
       name: Enable Coursier Cache
 
-    - name: Git secrets setup #The Broad requires git-secrets be setup. The Secrets check below veritfies that the setup worked.
+    #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
+    - name: Git secrets setup 
       run: |
         git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
         cd ~/git-secrets
@@ -87,18 +92,23 @@ jobs:
         ./minnie-kenny.sh --force
         git secrets --scan-history
 
+    #Clone the cromwell repo to this VM.
     - name: Clone Cromwell
       uses: actions/checkout@v3
       with:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+
+    #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
     - name: Setup JDK
       uses: actions/setup-java@v3
       with:
         distribution: temurin
         java-version: 11
         cache: sbt
-    - name: Run tests #Invoke SBT with an argument asking it to run a specific test in a specific sbt project. 
+
+    #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
+    - name: Run tests 
       run: |
         set -e
         sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file

From 3a158eaded488a5387c0244c97e76cd1f377a2be Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 26 Jan 2023 17:04:12 -0500
Subject: [PATCH 054/213] rename and polish

---
 .../{basic_unit_test.yml => cromwell_unit_tests.yml} | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)
 rename .github/workflows/{basic_unit_test.yml => cromwell_unit_tests.yml} (86%)

diff --git a/.github/workflows/basic_unit_test.yml b/.github/workflows/cromwell_unit_tests.yml
similarity index 86%
rename from .github/workflows/basic_unit_test.yml
rename to .github/workflows/cromwell_unit_tests.yml
index 4bde51e6db9..896cfce6908 100644
--- a/.github/workflows/basic_unit_test.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -1,10 +1,10 @@
-name: 'Basic Unit Test'
+name: 'Cromwell unit tests'
 
 #This github action runs all of Cromwell's unit tests.
 #A matrix strategy is used so that each subproject can be unit tested in parallel with all other subprojects. 
 
 #This is what shows up in the github workflows page as the title. 
-run-name: ${{ github.actor }} running Cromwell sbt Unit Tests.
+run-name: ${{ github.actor }} running Cromwell sbt unit tests.
 
 #What will trigger the workflow to run. 
 on:
@@ -15,8 +15,9 @@ on:
 permissions: 
   contents: read
 
+#This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
 jobs:
-  build-and-test: #This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
+  build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
       matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
@@ -69,11 +70,12 @@ jobs:
         wom,
         womtool]
 
-    runs-on: ubuntu-latest #Note: This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
+    #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
+    runs-on: ubuntu-latest
 
     steps:
 
-    #Allows this github action to use a cache to store stuff like Java and SBT files between runs.
+    #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
     - uses: actions/checkout@v3
       name: Checkout Coursier Cache
     - uses: coursier/cache-action@v6  

From 4e0821c77a0a36950c26a3e07fbfd903f7b5ee8e Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:06:31 -0500
Subject: [PATCH 055/213] this will not work

---
 .github/workflows/cromwell_unit_tests.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 896cfce6908..a0b95dbbf39 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -17,6 +17,15 @@ permissions:
 
 #This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
 jobs:
+  generate-sbt-project-array:
+    runs-on: ubuntu-latest
+    steps:
+      -id: build-array
+      -run: output=$(sbt projects \
+    | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" \
+    | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+      -run: echo $output
+
   build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.

From a1b4f4bb028facb98aaadefd01ad494ccbc0d974 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:08:19 -0500
Subject: [PATCH 056/213] newlines

---
 .github/workflows/cromwell_unit_tests.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index a0b95dbbf39..d05a58e76a0 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -21,9 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       -id: build-array
-      -run: output=$(sbt projects \
-    | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" \
-    | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+      -run: output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
       -run: echo $output
 
   build-and-test: 

From 8076020e5e7a646b8258496ab479b9aceab65f0a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:09:38 -0500
Subject: [PATCH 057/213] yaml

---
 .github/workflows/cromwell_unit_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index d05a58e76a0..a40a9a7d8e4 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -21,8 +21,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       -id: build-array
-      -run: output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
-      -run: echo $output
+       run: output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+       run: echo $output
 
   build-and-test: 
     strategy:

From d00fe600ce9b134429e1954072bd46af11be4029 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:11:27 -0500
Subject: [PATCH 058/213] error lol

---
 .github/workflows/cromwell_unit_tests.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index a40a9a7d8e4..bc0003901ac 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -22,8 +22,6 @@ jobs:
     steps:
       -id: build-array
        run: output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
-       run: echo $output
-
   build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.

From 9272636629ae3733448dbce771235c33f98d1514 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:12:38 -0500
Subject: [PATCH 059/213] pipe

---
 .github/workflows/cromwell_unit_tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index bc0003901ac..9a140269f50 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -21,7 +21,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       -id: build-array
-       run: output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+       run: | 
+       output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
   build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.

From 2ccbc76bf9982e46151c0f4bb3908759500db2e0 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:15:10 -0500
Subject: [PATCH 060/213] one step closer

---
 .github/workflows/cromwell_unit_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 9a140269f50..a5c6b681c4e 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -20,8 +20,8 @@ jobs:
   generate-sbt-project-array:
     runs-on: ubuntu-latest
     steps:
-      -id: build-array
-       run: | 
+      - name: build-array
+       run: |
        output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
   build-and-test: 
     strategy:

From 602c5eee9e78fdddcd5eece4a9dc322837f43000 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:16:51 -0500
Subject: [PATCH 061/213] idk

---
 .github/workflows/cromwell_unit_tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index a5c6b681c4e..d581d715631 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -21,7 +21,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: build-array
-       run: |
+      id: step_one
+      run: |
        output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
   build-and-test: 
     strategy:

From 53df19c38b26f2d83da7b73af3efa77318bc5529 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:18:40 -0500
Subject: [PATCH 062/213] syntax why

---
 .github/workflows/cromwell_unit_tests.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index d581d715631..4ee6cb6e637 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -18,8 +18,11 @@ permissions:
 #This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
 jobs:
   generate-sbt-project-array:
+
     runs-on: ubuntu-latest
+
     steps:
+    
       - name: build-array
       id: step_one
       run: |

From cd78e005202513c8ebeae7da06a9c183d95e071f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:21:35 -0500
Subject: [PATCH 063/213] yeye

---
 .github/workflows/cromwell_unit_tests.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 4ee6cb6e637..8b4e6f39aed 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -22,11 +22,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    
-      - name: build-array
-      id: step_one
+      - name: Do the thing
       run: |
        output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+       echo $output
   build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.

From 9a93df0e21d4a69e51e2c7ed472812909db319a5 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:23:17 -0500
Subject: [PATCH 064/213] back to basics

---
 .github/workflows/cromwell_unit_tests.yml | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 8b4e6f39aed..0a9538a737b 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -17,15 +17,6 @@ permissions:
 
 #This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
 jobs:
-  generate-sbt-project-array:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Do the thing
-      run: |
-       output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
-       echo $output
   build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
@@ -119,6 +110,12 @@ jobs:
         cache: sbt
 
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
+
+    - name: Do the thing
+      run: |
+       output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+       echo $output
+
     - name: Run tests 
       run: |
         set -e

From b6916810dd66cd7b4d2dc545645d76ffff513c4f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:32:37 -0500
Subject: [PATCH 065/213] advanced techniques

---
 .github/workflows/cromwell_unit_tests.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 0a9538a737b..7f4fc097d05 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,9 +112,11 @@ jobs:
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
 
     - name: Do the thing
-      run: |
-       output=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
-       echo $output
+       run: |
+       echo "SBT_PROJECTS=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+
+    - name: Test the thing
+      run: echo ${{ env.SBT_PROJECTS }}
 
     - name: Run tests 
       run: |

From 897bb7a39c71f89c99a2991360c5c89c0009ebb9 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:35:02 -0500
Subject: [PATCH 066/213] this wont work either

---
 .github/workflows/cromwell_unit_tests.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 7f4fc097d05..64ade9fcc84 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -109,8 +109,6 @@ jobs:
         java-version: 11
         cache: sbt
 
-    #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
-
     - name: Do the thing
        run: |
        echo "SBT_PROJECTS=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
@@ -118,6 +116,7 @@ jobs:
     - name: Test the thing
       run: echo ${{ env.SBT_PROJECTS }}
 
+    #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
     - name: Run tests 
       run: |
         set -e

From 025eea83ad8e3a7c24ae372507433c2922a83bce Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:36:18 -0500
Subject: [PATCH 067/213] nope

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 64ade9fcc84..920e871e4ac 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -110,7 +110,7 @@ jobs:
         cache: sbt
 
     - name: Do the thing
-       run: |
+      run: |
        echo "SBT_PROJECTS=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing

From 89a560781375ab3899e7171670095f83dae6cecb Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:41:07 -0500
Subject: [PATCH 068/213] try again

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 920e871e4ac..46f28e69fec 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -111,7 +111,7 @@ jobs:
 
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects | sed -e "s/^\[info\]\s:*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+       echo "SBT_PROJECTS=$(sbt projects| sed -e "s/^\[info\][[:blank:]]*\([-_A-Za-z0-9]*\)$/\1/g" grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: echo ${{ env.SBT_PROJECTS }}

From f155b4982b2321358404d1a024af0faa9cd68b9c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:44:09 -0500
Subject: [PATCH 069/213] aisd

---
 .github/workflows/cromwell_unit_tests.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 46f28e69fec..8053e8d40e3 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -111,10 +111,11 @@ jobs:
 
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects| sed -e "s/^\[info\][[:blank:]]*\([-_A-Za-z0-9]*\)$/\1/g" grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+       echo "SBT_PROJECTS=$(sbt projects| sed -e "s/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g" grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
-      run: echo ${{ env.SBT_PROJECTS }}
+      run: |
+        echo ${{ env.SBT_PROJECTS }}
 
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
     - name: Run tests 

From f28381ed52a8264516e7ae5569bd775583013e71 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:45:45 -0500
Subject: [PATCH 070/213] pipe got lost

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 8053e8d40e3..5ea92299536 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -111,7 +111,7 @@ jobs:
 
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects| sed -e "s/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g" grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+       echo "SBT_PROJECTS=$(sbt projects| sed -e "s/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From e978ad49f854c64a1aa10bf02b87dc4e43b3f7e0 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:56:49 -0500
Subject: [PATCH 071/213] quotatsions

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 5ea92299536..3ce32a57985 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -111,7 +111,7 @@ jobs:
 
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects| sed -e "s/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g" | grep -v "^\[info\].*" | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+       echo "SBT_PROJECTS=$(sbt projects| sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*'' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From e4f6f825c8416103317985645fe3706f25ada954 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 14:59:26 -0500
Subject: [PATCH 072/213] trying

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 3ce32a57985..d609d9f444d 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -111,7 +111,7 @@ jobs:
 
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects| sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*'' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+       echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\][[:blank:]]*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 8d702dea2940154b68025bfd629b6b7c4e28096a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 15:02:04 -0500
Subject: [PATCH 073/213] \s

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index d609d9f444d..369750ff16f 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -111,7 +111,7 @@ jobs:
 
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\][[:blank:]]*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+       echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 778af442e1722afa7ee787ac7ba89fb054c5000f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 15:07:49 -0500
Subject: [PATCH 074/213] rome was built from the command line

---
 .github/workflows/cromwell_unit_tests.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 369750ff16f..408dd71607a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -109,10 +109,11 @@ jobs:
         java-version: 11
         cache: sbt
 
+    # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-       echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
-
+      echo "SBT_PROJECTS=$(sbt projects)"
+      
     - name: Test the thing
       run: |
         echo ${{ env.SBT_PROJECTS }}

From 7eff6891764dc2564caf5ab9884ac2034f232eb2 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 15:09:03 -0500
Subject: [PATCH 075/213] i cant keep coming up with commit messages

---
 .github/workflows/cromwell_unit_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 408dd71607a..fc43b7ff64e 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,8 +112,8 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-      echo "SBT_PROJECTS=$(sbt projects)"
-      
+        echo "SBT_PROJECTS=$(sbt projects)"  >> $GITHUB_ENV
+
     - name: Test the thing
       run: |
         echo ${{ env.SBT_PROJECTS }}

From a62a7549c916a92c225ad6f53124dda9ec5e4faf Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 30 Jan 2023 15:29:33 -0500
Subject: [PATCH 076/213] working?

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index fc43b7ff64e..e5ce2ba6a51 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects)"  >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed -e 's/\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 11101fb588ec868a735354e97a99d587be70f5bb Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 15:47:04 -0500
Subject: [PATCH 077/213] Escape asterisks

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index e5ce2ba6a51..60e9abafd8a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed -e 's/\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed -e 's/\[info\]\s\*\([-_A-Za-z0-9]\*\)$/\1/g' | grep -v '\[info\].\*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From c4341daf0c2729e04586953a5c3becfcece8f4bf Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 15:55:19 -0500
Subject: [PATCH 078/213] Does this work?

---
 .github/workflows/cromwell_unit_tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 60e9abafd8a..5f204bc1d96 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,8 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed -e 's/\[info\]\s\*\([-_A-Za-z0-9]\*\)$/\1/g' | grep -v '\[info\].\*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+        SBT_PROJ=$(sbt projects | sed 's/\[info\]\s\*\([-_A-Za-z0-9]\*\)$/\1/g' | grep -v '\[info\]' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+        echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 39e62706066968151b392ca8d2459393faaef07e Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:00:37 -0500
Subject: [PATCH 079/213] Also escape dollar sign

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 5f204bc1d96..f665d155aaf 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[info\]\s\*\([-_A-Za-z0-9]\*\)$/\1/g' | grep -v '\[info\]' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+        SBT_PROJ=$(sbt projects | sed 's/\[info\]\s\*\([-_A-Za-z0-9]\*\)\$/\1/g' | grep -v '\[info\]' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From ceed50eb1979fc605860106a98025a0eed78999b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:14:30 -0500
Subject: [PATCH 080/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index f665d155aaf..56b03f5c08e 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[info\]\s\*\([-_A-Za-z0-9]\*\)\$/\1/g' | grep -v '\[info\]' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+        SBT_PROJ=$(sbt projects | sed 's/\[info\]/INFO/g' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From df46ef6f0d8a09efc2e9109c68265b2bcda556ac Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:16:44 -0500
Subject: [PATCH 081/213] More escaping

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 56b03f5c08e..3fdee572999 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[info\]/INFO/g' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+        SBT_PROJ=$(sbt projects | sed 's/\\[info\\]/INFO/g' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From de6704baa659fbe69a72c831064da93a294afc76 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:19:51 -0500
Subject: [PATCH 082/213] Less escaping

---
 .github/workflows/cromwell_unit_tests.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 3fdee572999..894d3e4eddf 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\\[info\\]/INFO/g' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+        SBT_PROJ=$(sbt projects | sed 's/[info]/INFO/g' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing
@@ -120,7 +120,7 @@ jobs:
         echo ${{ env.SBT_PROJECTS }}
 
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
-    - name: Run tests 
-      run: |
-        set -e
-        sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file
+#    - name: Run tests
+#      run: |
+#        set -e
+#        sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file

From 9afc8c98e0644940ac5da2850af6d9a1b10707db Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:26:52 -0500
Subject: [PATCH 083/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 98 +++++++++++------------
 1 file changed, 49 insertions(+), 49 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 894d3e4eddf..2836d73d5ed 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -21,54 +21,54 @@ jobs:
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
       matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
-        sbtSubProject: [awsBackend,
-        awsS3FileSystem,
-        azureBlobFileSystem,
-        backend,
-        centaur,
-        cloud-nio-impl-drs,
-        cloud-nio-impl-ftp,
-        cloud-nio-spi,
-        cloud-nio-util,
-        cloudSupport,
-        common,
-        core,
-        cromiam,
-        cromwell-drs-localizer,
-        cromwellApiClient,
-        databaseMigration,
-        databaseSql,
-        dockerHashing,
-        drsFileSystem,
-        engine,
-        ftpFileSystem,
-        gcsFileSystem,
-        googlePipelinesCommon,
-        googlePipelinesV2Alpha1,
-        googlePipelinesV2Beta,
-        httpFileSystem,
-        languageFactoryCore,
-        perf,
-        server,
-        services,
-        sfsBackend,
-        sraFileSystem,
-        tesBackend,
-        wdlBiscayneLanguageFactory,
-        wdlDraft2LanguageFactory,
-        wdlDraft3LanguageFactory,
-        wdlModelBiscayne,
-        wdlModelDraft2,
-        wdlModelDraft3,
-        wdlNewBaseTransforms,
-        wdlSharedModel,
-        wdlSharedTransforms,
-        wdlTransformsBiscayne,
-        wdlTransformsDraft2,
-        wdlTransformsDraft3,
-        wes2cromwell,
-        wom,
-        womtool]
+        sbtSubProject: [awsBackend]
+#        awsS3FileSystem,
+#        azureBlobFileSystem,
+#        backend,
+#        centaur,
+#        cloud-nio-impl-drs,
+#        cloud-nio-impl-ftp,
+#        cloud-nio-spi,
+#        cloud-nio-util,
+#        cloudSupport,
+#        common,
+#        core,
+#        cromiam,
+#        cromwell-drs-localizer,
+#        cromwellApiClient,
+#        databaseMigration,
+#        databaseSql,
+#        dockerHashing,
+#        drsFileSystem,
+#        engine,
+#        ftpFileSystem,
+#        gcsFileSystem,
+#        googlePipelinesCommon,
+#        googlePipelinesV2Alpha1,
+#        googlePipelinesV2Beta,
+#        httpFileSystem,
+#        languageFactoryCore,
+#        perf,
+#        server,
+#        services,
+#        sfsBackend,
+#        sraFileSystem,
+#        tesBackend,
+#        wdlBiscayneLanguageFactory,
+#        wdlDraft2LanguageFactory,
+#        wdlDraft3LanguageFactory,
+#        wdlModelBiscayne,
+#        wdlModelDraft2,
+#        wdlModelDraft3,
+#        wdlNewBaseTransforms,
+#        wdlSharedModel,
+#        wdlSharedTransforms,
+#        wdlTransformsBiscayne,
+#        wdlTransformsDraft2,
+#        wdlTransformsDraft3,
+#        wes2cromwell,
+#        wom,
+#        womtool]
 
     #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/[info]/INFO/g' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')
+        SBT_PROJ=$(sbt projects | sed 's/\[info\]/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From c9640c607bdc3ffcf455972610b2427e6da89ed0 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:31:34 -0500
Subject: [PATCH 084/213] EVEN MORE ESCAPING

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 2836d73d5ed..0f4262cd343 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[info\]/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\\\[info\\\]/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 29cc772d55d0dbcd41d8a3a92fc4a07fa35c4f9b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:42:17 -0500
Subject: [PATCH 085/213] What if we didn't use brackets at all

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 0f4262cd343..bf89cc8278b 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\\\[info\\\]/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/^.info./INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From fc01ca7909639f1d419c847378b731630a860887 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:47:30 -0500
Subject: [PATCH 086/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index bf89cc8278b..5fcc2f47de7 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/^.info./INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/.info./INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 76290cd8dc2cbb25867999560fac3654a9faf80d Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:54:32 -0500
Subject: [PATCH 087/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 5fcc2f47de7..b498fc2e743 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/.info./INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/^.info.\s*/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From c924572ef4de85e3bfc72e937ada5afe9253ebf0 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:56:10 -0500
Subject: [PATCH 088/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index b498fc2e743..9467ab299b5 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/^.info.\s*/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\^\.info\.\\s*/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 997f5a7155176559e613c8c1f13af0cb5114b848 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 16:58:19 -0500
Subject: [PATCH 089/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 9467ab299b5..fbaabeda996 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\^\.info\.\\s*/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\\^\\.info\\.\\\\s*/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 3cfee4ad8c1ea540c230dd3875cf34000e563e6b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 17:00:49 -0500
Subject: [PATCH 090/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index fbaabeda996..0504759f273 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\\^\\.info\\.\\\\s*/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/info/INFO/g')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 04709630e306c7182e19ffb87d9293520b96f221 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 17:05:46 -0500
Subject: [PATCH 091/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 0504759f273..33b6548c147 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/info/INFO/g')
+        SBT_PROJ=$(sbt projects | sed 's/\.info\./INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 5d11931eb0b557abab0f9d46ee788e62581bc336 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 17:07:27 -0500
Subject: [PATCH 092/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 33b6548c147..5fcc2f47de7 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\.info\./INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/.info./INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From e83e7a4a6073f5318d23b1fd79e46cfa4e3eea54 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:07:47 -0500
Subject: [PATCH 093/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 5fcc2f47de7..f7632dd52ee 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/.info./INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/^\[.*info.*\]/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 678f77a456e11d5a5bfec1aeaff4eb83e9584b82 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:11:21 -0500
Subject: [PATCH 094/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index f7632dd52ee..4f5f4afff7f 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/^\[.*info.*\]/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/^\\\[.*info.*\\\]/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From cc209c4398bafad5246ad7eacba558d2d2cffb41 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:14:28 -0500
Subject: [PATCH 095/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 4f5f4afff7f..7ffe1fcc8f7 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/^\\\[.*info.*\\\]/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\[.*info.*\]/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 069c1a6de4f1f1df82e3764e5225a50146ee250d Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:17:21 -0500
Subject: [PATCH 096/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 7ffe1fcc8f7..34e7088af79 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[.*info.*\]/INFO/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\[.*info.*\]\s*(.*)/\1/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 8368318174831cc9875bab49ebb8be2bba1dffd1 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:18:24 -0500
Subject: [PATCH 097/213] Testing

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 34e7088af79..9493c0182d1 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[.*info.*\]\s*(.*)/\1/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\[.*info.*\]\s*\(.*\)/\1/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From 9c8b38ce8091b3558528fae18bf48dc35717d23f Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:31:09 -0500
Subject: [PATCH 098/213] Remove color codes

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 9493c0182d1..3f9c5d1fb2a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\[.*info.*\]\s*\(.*\)/\1/g' | tr '\n', ',')
+        SBT_PROJ=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed 's/\[info\]/INFO/g' | tr '\n', ',')
         echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
 
     - name: Test the thing

From db128afb3a6d5a05772693e29f4bad797f3cf965 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:34:22 -0500
Subject: [PATCH 099/213] Try the whole thing

---
 .github/workflows/cromwell_unit_tests.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 3f9c5d1fb2a..325a392533d 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,8 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJ=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed 's/\[info\]/INFO/g' | tr '\n', ',')
-        echo "SBT_PROJECTS='${SBT_PROJ}'" >> $GITHUB_ENV
+        SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 461c0aa49e7448dd27947568f4d553e3ed717caf Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:36:50 -0500
Subject: [PATCH 100/213] Oops

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 325a392533d..e5556a05bc8 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -112,7 +112,7 @@ jobs:
     # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 6358c75e43135bd4af00cdd006abdb79164a5c1d Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:41:02 -0500
Subject: [PATCH 101/213] Revert test changes, remove trailing comma

---
 .github/workflows/cromwell_unit_tests.yml | 107 +++++++++++-----------
 1 file changed, 53 insertions(+), 54 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index e5556a05bc8..9e9e8387e52 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -21,54 +21,54 @@ jobs:
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
       matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
-        sbtSubProject: [awsBackend]
-#        awsS3FileSystem,
-#        azureBlobFileSystem,
-#        backend,
-#        centaur,
-#        cloud-nio-impl-drs,
-#        cloud-nio-impl-ftp,
-#        cloud-nio-spi,
-#        cloud-nio-util,
-#        cloudSupport,
-#        common,
-#        core,
-#        cromiam,
-#        cromwell-drs-localizer,
-#        cromwellApiClient,
-#        databaseMigration,
-#        databaseSql,
-#        dockerHashing,
-#        drsFileSystem,
-#        engine,
-#        ftpFileSystem,
-#        gcsFileSystem,
-#        googlePipelinesCommon,
-#        googlePipelinesV2Alpha1,
-#        googlePipelinesV2Beta,
-#        httpFileSystem,
-#        languageFactoryCore,
-#        perf,
-#        server,
-#        services,
-#        sfsBackend,
-#        sraFileSystem,
-#        tesBackend,
-#        wdlBiscayneLanguageFactory,
-#        wdlDraft2LanguageFactory,
-#        wdlDraft3LanguageFactory,
-#        wdlModelBiscayne,
-#        wdlModelDraft2,
-#        wdlModelDraft3,
-#        wdlNewBaseTransforms,
-#        wdlSharedModel,
-#        wdlSharedTransforms,
-#        wdlTransformsBiscayne,
-#        wdlTransformsDraft2,
-#        wdlTransformsDraft3,
-#        wes2cromwell,
-#        wom,
-#        womtool]
+        sbtSubProject: [awsBackend,
+                        awsS3FileSystem,
+                        azureBlobFileSystem,
+                        backend,
+                        centaur,
+                        cloud-nio-impl-drs,
+                        cloud-nio-impl-ftp,
+                        cloud-nio-spi,
+                        cloud-nio-util,
+                        cloudSupport,
+                        common,
+                        core,
+                        cromiam,
+                        cromwell-drs-localizer,
+                        cromwellApiClient,
+                        databaseMigration,
+                        databaseSql,
+                        dockerHashing,
+                        drsFileSystem,
+                        engine,
+                        ftpFileSystem,
+                        gcsFileSystem,
+                        googlePipelinesCommon,
+                        googlePipelinesV2Alpha1,
+                        googlePipelinesV2Beta,
+                        httpFileSystem,
+                        languageFactoryCore,
+                        perf,
+                        server,
+                        services,
+                        sfsBackend,
+                        sraFileSystem,
+                        tesBackend,
+                        wdlBiscayneLanguageFactory,
+                        wdlDraft2LanguageFactory,
+                        wdlDraft3LanguageFactory,
+                        wdlModelBiscayne,
+                        wdlModelDraft2,
+                        wdlModelDraft3,
+                        wdlNewBaseTransforms,
+                        wdlSharedModel,
+                        wdlSharedTransforms,
+                        wdlTransformsBiscayne,
+                        wdlTransformsDraft2,
+                        wdlTransformsDraft3,
+                        wes2cromwell,
+                        wom,
+                        womtool]
 
     #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
@@ -109,17 +109,16 @@ jobs:
         java-version: 11
         cache: sbt
 
-    # echo "SBT_PROJECTS=$(sbt projects | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.,$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |
         echo ${{ env.SBT_PROJECTS }}
 
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
-#    - name: Run tests
-#      run: |
-#        set -e
-#        sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file
+    - name: Run tests
+      run: |
+        set -e
+        sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file

From 52ee24fe3384528423e03b04311487fd611c626b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 30 Jan 2023 19:45:47 -0500
Subject: [PATCH 102/213] Leave comma to deal with later, add comment

---
 .github/workflows/cromwell_unit_tests.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 9e9e8387e52..fb04d5eacd0 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -109,9 +109,11 @@ jobs:
         java-version: 11
         cache: sbt
 
+    #Parse the sbt-generated list of projects into a YAML array. Note that we strip
+    #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.,$/]\n/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 15d93027a4daa161739585598dda2e84f786db0d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 10:45:37 -0500
Subject: [PATCH 103/213] here goes nothing

---
 .github/set_up_cromwell_action/action.yml | 43 +++++++++++++++++++++++
 .github/workflows/cromwell_unit_tests.yml | 36 ++-----------------
 2 files changed, 45 insertions(+), 34 deletions(-)
 create mode 100644 .github/set_up_cromwell_action/action.yml

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
new file mode 100644
index 00000000000..55ead7a09e9
--- /dev/null
+++ b/.github/set_up_cromwell_action/action.yml
@@ -0,0 +1,43 @@
+name: 'Set Up Cromwell Steps'
+#This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
+#These steps are meant to be re-used and  invoked by other Github Action Workflows that wish to have cromwell up-and-running before they do their thing. 
+
+runs:
+  using: "composite" # <-- this allows these steps to be used by other workflows.
+  steps:
+      #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
+      - uses: actions/checkout@v3
+        name: Checkout Coursier Cache
+      - uses: coursier/cache-action@v6  
+        name: Enable Coursier Cache
+
+      #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
+      - name: Git secrets setup 
+        run: |
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          cd ~/git-secrets
+          git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
+          sudo make install
+        shell: bash
+
+      - name: Secrets check
+        run: |
+          sudo ln -s "$(which echo)" /usr/local/bin/say
+          ./minnie-kenny.sh --force
+          git secrets --scan-history
+        shell: bash
+
+      #Clone the cromwell repo to this VM.
+      - name: Clone Cromwell
+        uses: actions/checkout@v3
+        with:
+          repository: broadinstitute/cromwell
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+
+      #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
+      - name: Setup JDK
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+          cache: sbt
diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index fb04d5eacd0..de59a3ecf77 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -74,40 +74,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-
-    #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
-    - uses: actions/checkout@v3
-      name: Checkout Coursier Cache
-    - uses: coursier/cache-action@v6  
-      name: Enable Coursier Cache
-
-    #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
-    - name: Git secrets setup 
-      run: |
-        git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
-        cd ~/git-secrets
-        git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
-        sudo make install
-    - name: Secrets check
-      run: |
-        sudo ln -s "$(which echo)" /usr/local/bin/say
-        ./minnie-kenny.sh --force
-        git secrets --scan-history
-
-    #Clone the cromwell repo to this VM.
-    - name: Clone Cromwell
-      uses: actions/checkout@v3
-      with:
-        repository: broadinstitute/cromwell
-        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
-
-    #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
-    - name: Setup JDK
-      uses: actions/setup-java@v3
-      with:
-        distribution: temurin
-        java-version: 11
-        cache: sbt
+    	- uses: actions/checkout@v3 # required first to checkout the repo
+	    - uses: ./.github/set_up_cromwell_action
 
     #Parse the sbt-generated list of projects into a YAML array. Note that we strip
     #invisible color codes out of the `sbt projects` output.

From bf91a067a9c0f5f244af1198f220b9201b9ca66c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 10:47:31 -0500
Subject: [PATCH 104/213] whitespace

---
 .github/workflows/cromwell_unit_tests.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index de59a3ecf77..5b5b2401037 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -74,9 +74,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    	- uses: actions/checkout@v3 # required first to checkout the repo
-	    - uses: ./.github/set_up_cromwell_action
-
+    - uses: actions/checkout@v3 # required first to checkout the repo
+    - uses: ./.github/set_up_cromwell_action
     #Parse the sbt-generated list of projects into a YAML array. Note that we strip
     #invisible color codes out of the `sbt projects` output.
     - name: Do the thing

From 74796d45f948d7d3825927c3245fd6c918c85986 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 10:54:59 -0500
Subject: [PATCH 105/213] using secrets

---
 .github/set_up_cromwell_action/action.yml | 6 +++++-
 .github/workflows/cromwell_unit_tests.yml | 3 +++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 55ead7a09e9..67944c59c44 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -1,4 +1,8 @@
 name: 'Set Up Cromwell Steps'
+description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
+inputs:
+  cromwell_repo_token:
+    required: true
 #This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
 #These steps are meant to be re-used and  invoked by other Github Action Workflows that wish to have cromwell up-and-running before they do their thing. 
 
@@ -32,7 +36,7 @@ runs:
         uses: actions/checkout@v3
         with:
           repository: broadinstitute/cromwell
-          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+          token: ${{ inputs.cromwell_repo_token }}
 
       #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
       - name: Setup JDK
diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 5b5b2401037..2d2cb028739 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -76,6 +76,9 @@ jobs:
     steps:
     - uses: actions/checkout@v3 # required first to checkout the repo
     - uses: ./.github/set_up_cromwell_action
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+
     #Parse the sbt-generated list of projects into a YAML array. Note that we strip
     #invisible color codes out of the `sbt projects` output.
     - name: Do the thing

From 247f412423ee007d58f38c60aecdb6fb2b9d649f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:00:54 -0500
Subject: [PATCH 106/213] comments

---
 .github/set_up_cromwell_action/action.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 67944c59c44..038aa2b0346 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -1,10 +1,10 @@
+#This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
+#These steps are meant to be re-used and invoked by other Github Action Workflows
 name: 'Set Up Cromwell Steps'
 description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
 inputs:
-  cromwell_repo_token:
+  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
     required: true
-#This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
-#These steps are meant to be re-used and  invoked by other Github Action Workflows that wish to have cromwell up-and-running before they do their thing. 
 
 runs:
   using: "composite" # <-- this allows these steps to be used by other workflows.

From d184b6f735efe21c37e59d01aea33a7ab15e8430 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:15:30 -0500
Subject: [PATCH 107/213] yolo

---
 .github/workflows/cromwell_unit_tests.yml | 76 +++++++----------------
 1 file changed, 24 insertions(+), 52 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 2d2cb028739..0459d837cfa 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -15,60 +15,34 @@ on:
 permissions: 
   contents: read
 
-#This job is spawned once for each subproject in the matrix below. Each iteration will set up a cache, git secrets, and java before running unit tests for that subproject.
 jobs:
+  generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
+  runs-on: ubuntu-latest
+  steps:
+    - uses: actions/checkout@v3 # required first to checkout the repo
+    - uses: ./.github/set_up_cromwell_action
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+
+    #Parse the sbt-generated list of projects into a YAML array. Note that we strip
+    #invisible color codes out of the `sbt projects` output.
+    - name: Do the thing
+      run: |
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+
+    - name: Test the thing
+      run: |
+        echo ${{ env.SBT_PROJECTS }}
+
+    outputs:
+      subproject-matrix: ${{ env.SBT_PROJECTS }}
+
   build-and-test: 
+    needs: generate-subproject-matrix
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
       matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
-        sbtSubProject: [awsBackend,
-                        awsS3FileSystem,
-                        azureBlobFileSystem,
-                        backend,
-                        centaur,
-                        cloud-nio-impl-drs,
-                        cloud-nio-impl-ftp,
-                        cloud-nio-spi,
-                        cloud-nio-util,
-                        cloudSupport,
-                        common,
-                        core,
-                        cromiam,
-                        cromwell-drs-localizer,
-                        cromwellApiClient,
-                        databaseMigration,
-                        databaseSql,
-                        dockerHashing,
-                        drsFileSystem,
-                        engine,
-                        ftpFileSystem,
-                        gcsFileSystem,
-                        googlePipelinesCommon,
-                        googlePipelinesV2Alpha1,
-                        googlePipelinesV2Beta,
-                        httpFileSystem,
-                        languageFactoryCore,
-                        perf,
-                        server,
-                        services,
-                        sfsBackend,
-                        sraFileSystem,
-                        tesBackend,
-                        wdlBiscayneLanguageFactory,
-                        wdlDraft2LanguageFactory,
-                        wdlDraft3LanguageFactory,
-                        wdlModelBiscayne,
-                        wdlModelDraft2,
-                        wdlModelDraft3,
-                        wdlNewBaseTransforms,
-                        wdlSharedModel,
-                        wdlSharedTransforms,
-                        wdlTransformsBiscayne,
-                        wdlTransformsDraft2,
-                        wdlTransformsDraft3,
-                        wes2cromwell,
-                        wom,
-                        womtool]
+        sbtSubProject: ${{ needs.generate-subproject-matrix.outputs.subproject-matrix }}
 
     #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
@@ -85,9 +59,7 @@ jobs:
       run: |
         echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
-    - name: Test the thing
-      run: |
-        echo ${{ env.SBT_PROJECTS }}
+
 
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
     - name: Run tests

From 68fc894f375d6f6aaf939c6d5cccccc2c1e8ba8c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:17:52 -0500
Subject: [PATCH 108/213] indent

---
 .github/workflows/cromwell_unit_tests.yml | 32 +++++++++++------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 0459d837cfa..c0be60a5b12 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -17,25 +17,25 @@ permissions:
 
 jobs:
   generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
-  runs-on: ubuntu-latest
-  steps:
-    - uses: actions/checkout@v3 # required first to checkout the repo
-    - uses: ./.github/set_up_cromwell_action
-      with:
-        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3 # required first to checkout the repo
+      - uses: ./.github/set_up_cromwell_action
+        with:
+          cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
 
-    #Parse the sbt-generated list of projects into a YAML array. Note that we strip
-    #invisible color codes out of the `sbt projects` output.
-    - name: Do the thing
-      run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+      #Parse the sbt-generated list of projects into a YAML array. Note that we strip
+      #invisible color codes out of the `sbt projects` output.
+      - name: Do the thing
+        run: |
+          echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
-    - name: Test the thing
-      run: |
-        echo ${{ env.SBT_PROJECTS }}
+      - name: Test the thing
+        run: |
+          echo ${{ env.SBT_PROJECTS }}
 
-    outputs:
-      subproject-matrix: ${{ env.SBT_PROJECTS }}
+      outputs:
+        subproject-matrix: ${{ env.SBT_PROJECTS }}
 
   build-and-test: 
     needs: generate-subproject-matrix

From 962c04f2846e53a238bbc326d1caf57e0c4c1277 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:20:31 -0500
Subject: [PATCH 109/213] idgetit

---
 .github/workflows/cromwell_unit_tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index c0be60a5b12..ae29152f51b 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -18,6 +18,7 @@ permissions:
 jobs:
   generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
     runs-on: ubuntu-latest
+    
     steps:
       - uses: actions/checkout@v3 # required first to checkout the repo
       - uses: ./.github/set_up_cromwell_action

From 0302bc6878853938874a5f8291dd284dbec4c3fe Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:22:50 -0500
Subject: [PATCH 110/213] indent

---
 .github/workflows/cromwell_unit_tests.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index ae29152f51b..c0be60a5b12 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -18,7 +18,6 @@ permissions:
 jobs:
   generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
     runs-on: ubuntu-latest
-    
     steps:
       - uses: actions/checkout@v3 # required first to checkout the repo
       - uses: ./.github/set_up_cromwell_action

From afe4d3b0ad135be035926146ab0ece61c4f29ebe Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:25:25 -0500
Subject: [PATCH 111/213] this is dumb

---
 .github/workflows/cromwell_unit_tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index c0be60a5b12..1eea6ef6ae2 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -17,6 +17,7 @@ permissions:
 
 jobs:
   generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
+    name: Get sbt subprojects
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3 # required first to checkout the repo

From 01fbecec520953f8e6b3b48e5dc7045a7ba52a89 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:26:33 -0500
Subject: [PATCH 112/213] copypasta

---
 .github/workflows/cromwell_unit_tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 1eea6ef6ae2..ae9ef77e87a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -19,6 +19,7 @@ jobs:
   generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
     name: Get sbt subprojects
     runs-on: ubuntu-latest
+
     steps:
       - uses: actions/checkout@v3 # required first to checkout the repo
       - uses: ./.github/set_up_cromwell_action

From 37bca130ed7138aa101deaf573abb7bb8410dee1 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:28:55 -0500
Subject: [PATCH 113/213] asd

---
 .github/workflows/cromwell_unit_tests.yml | 27 ++++++++++-------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index ae9ef77e87a..41c69f3e9ad 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -19,25 +19,24 @@ jobs:
   generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
     name: Get sbt subprojects
     runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v3 # required first to checkout the repo
-      - uses: ./.github/set_up_cromwell_action
-        with:
-          cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+    - uses: actions/checkout@v3 # required first to checkout the repo
+    - uses: ./.github/set_up_cromwell_action
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
 
       #Parse the sbt-generated list of projects into a YAML array. Note that we strip
       #invisible color codes out of the `sbt projects` output.
-      - name: Do the thing
-        run: |
-          echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+    - name: Do the thing
+      run: |
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
-      - name: Test the thing
-        run: |
-          echo ${{ env.SBT_PROJECTS }}
+    - name: Test the thing
+        un: |
+        echo ${{ env.SBT_PROJECTS }}
 
-      outputs:
-        subproject-matrix: ${{ env.SBT_PROJECTS }}
+    outputs:
+      subproject-matrix: ${{ env.SBT_PROJECTS }}
 
   build-and-test: 
     needs: generate-subproject-matrix
@@ -61,8 +60,6 @@ jobs:
       run: |
         echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
-
-
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
     - name: Run tests
       run: |

From 019f33323c0512c3b431796a3f2901704927a22b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:29:39 -0500
Subject: [PATCH 114/213] actionable

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 41c69f3e9ad..1da6957df84 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -32,7 +32,7 @@ jobs:
         echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
-        un: |
+        run: |
         echo ${{ env.SBT_PROJECTS }}
 
     outputs:

From 5aa1271461543ba9a4d31e172470b2937434839c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:31:07 -0500
Subject: [PATCH 115/213] whitespace

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 1da6957df84..5bacb811975 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -32,7 +32,7 @@ jobs:
         echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
 
     - name: Test the thing
-        run: |
+      run: |
         echo ${{ env.SBT_PROJECTS }}
 
     outputs:

From e9dc5f631d4977f0430114ffb07ad432785e1c6f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:41:09 -0500
Subject: [PATCH 116/213] remove newline:

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 5bacb811975..1e746d661fa 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 857ad95da51adb6f99111c31bc0210abecd14f58 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:50:57 -0500
Subject: [PATCH 117/213] lets seeeeee

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 1e746d661fa..8c9351df436 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,[^,]*\]$/\]/g')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 97b3666554044093501ead2e6b48b99f95dd0c5f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 11:53:20 -0500
Subject: [PATCH 118/213] what is even in there:

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 8c9351df436..c6013fda23a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,[^,]*\]$/\]/g')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 7fb8069ce6dbad2215ee4251ba052fc1cbacf372 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:01:52 -0500
Subject: [PATCH 119/213] the ol doubble commar

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index c6013fda23a..db97dc7b83c 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,,$/]/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From a78c30fb9143e4dcc3a2505b36c1fe43f73d9797 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:05:24 -0500
Subject: [PATCH 120/213] the double dot

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index db97dc7b83c..257a9cd2dab 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,,$/]/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/..$/]/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From f4d72160d600b70f9bc2ce20af9e3ce75ef682f3 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:11:16 -0500
Subject: [PATCH 121/213] dont ask questions

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 257a9cd2dab..0c5640a72e1 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/..$/]/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,{2,}/]/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 54aaee3292e0bc10b885522a0e58ada08fecf16d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:14:12 -0500
Subject: [PATCH 122/213] y

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 0c5640a72e1..af7baa835d9 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,{2,}/]/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,\{2,\}/]/g')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 8403b9f9b5bbb4c22346291c2ca041593b7f817f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:19:14 -0500
Subject: [PATCH 123/213] 2

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index af7baa835d9..691c5f52106 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/,\{2,\}/]/g')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{2\}$//')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From fcf9c8f2a1f9259a9aefc1a90aa09b6b503902bc Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:21:35 -0500
Subject: [PATCH 124/213] 5

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 691c5f52106..639669d0ffa 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{2\}$//')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{5\}$//')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From eaa48520b878ee4cea5aea22dbb471d9ba509b8d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:24:58 -0500
Subject: [PATCH 125/213] lol

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 639669d0ffa..c832c58de4d 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{5\}$//')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{6\}$/]/')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From 26091461d252dbfcacca656d6d8e758fe2cc8286 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 12:34:29 -0500
Subject: [PATCH 126/213] whitespoace

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index c832c58de4d..e301bfa3c87 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -29,7 +29,7 @@ jobs:
       #invisible color codes out of the `sbt projects` output.
     - name: Do the thing
       run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{6\}$/]/')" >> $GITHUB_ENV
+        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{6\}$/]/' | sed ':a; N; s/[[:space:]]//g; ta')" >> $GITHUB_ENV
 
     - name: Test the thing
       run: |

From f4837f80f6a2d69eba6f83f2af2f1408658f1e37 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 13:07:38 -0500
Subject: [PATCH 127/213] a

---
 .github/workflows/cromwell_unit_tests.yml | 74 +++++++++++++++--------
 1 file changed, 50 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index e301bfa3c87..7e7d684f399 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -16,34 +16,60 @@ permissions:
   contents: read
 
 jobs:
-  generate-subproject-matrix: #This job will invoke SBT to get a list of all subprojects in Cromwell. Later, this list will be used to teach each subproject in parallel.
-    name: Get sbt subprojects
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3 # required first to checkout the repo
-    - uses: ./.github/set_up_cromwell_action
-      with:
-        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
-
-      #Parse the sbt-generated list of projects into a YAML array. Note that we strip
-      #invisible color codes out of the `sbt projects` output.
-    - name: Do the thing
-      run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' |sed 's/.\{6\}$/]/' | sed ':a; N; s/[[:space:]]//g; ta')" >> $GITHUB_ENV
-
-    - name: Test the thing
-      run: |
-        echo ${{ env.SBT_PROJECTS }}
-
-    outputs:
-      subproject-matrix: ${{ env.SBT_PROJECTS }}
-
   build-and-test: 
-    needs: generate-subproject-matrix
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
       matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
-        sbtSubProject: ${{ needs.generate-subproject-matrix.outputs.subproject-matrix }}
+        sbtSubProject: [
+          awsBackend
+          awsS3FileSystem
+          azureBlobFileSystem
+          backend
+          centaur
+          cloud-nio-impl-drs
+          cloud-nio-impl-ftp
+          cloud-nio-spi
+          Cloud-nio-util
+          cloudSupport
+          common
+          core
+          cromiam
+          cromwell-drs-localizer
+          cromwellApiClient
+          databaseMigration
+          databaseSql
+          dockerHashing
+          drsFileSystem
+          engine
+          ftpFileSystem
+          gcsFileSystem
+          googlePipelinesCommon
+          googlePipelinesV2Alpha1
+          googlePipelinesV2Beta
+          httpFileSystem
+          languageFactoryCore
+          perf
+          root
+          server
+          services
+          sfsBackend
+          sraFileSystem
+          tesBackend
+          wdlBiscayneLanguageFactory
+          wdlDraft2LanguageFactory
+          wdlDraft3LanguageFactory
+          wdlModelBiscayne
+          wdlModelDraft2
+          wdlModelDraft3
+          wdlNewBaseTransforms
+          wdlSharedModel
+          wdlSharedTransforms
+          wdlTransformsBiscayne
+          wdlTransformsDraft2
+          wdlTransformsDraft3
+          wes2cromwell
+          wom
+          womtool]
 
     #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest

From 33fe63cf072b099130032a887d40803a0568a47b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 13:09:30 -0500
Subject: [PATCH 128/213] whoops

---
 .github/workflows/cromwell_unit_tests.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 7e7d684f399..f83798fa5cb 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -79,13 +79,7 @@ jobs:
     - uses: ./.github/set_up_cromwell_action
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
-
-    #Parse the sbt-generated list of projects into a YAML array. Note that we strip
-    #invisible color codes out of the `sbt projects` output.
-    - name: Do the thing
-      run: |
-        echo "SBT_PROJECTS=$(sbt projects | sed 's/\x1b\[[0-9;]*m//g' | sed -e 's/^\[info\]\s*\([-_A-Za-z0-9]*\)$/\1/g' | grep -v '^\[info\].*' | tr '\n', ',' | sed 's/^/[/' | sed 's/.$/]\n/')" >> $GITHUB_ENV
-
+  
     #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
     - name: Run tests
       run: |

From df0fbc7c5ebf50b663e1208ffe0b0b51e5db4fca Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 13:12:10 -0500
Subject: [PATCH 129/213] better formatting

---
 .github/workflows/cromwell_unit_tests.yml | 98 +++++++++++------------
 1 file changed, 48 insertions(+), 50 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index f83798fa5cb..ed704e960be 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -20,56 +20,54 @@ jobs:
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
       matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
-        sbtSubProject: [
-          awsBackend
-          awsS3FileSystem
-          azureBlobFileSystem
-          backend
-          centaur
-          cloud-nio-impl-drs
-          cloud-nio-impl-ftp
-          cloud-nio-spi
-          Cloud-nio-util
-          cloudSupport
-          common
-          core
-          cromiam
-          cromwell-drs-localizer
-          cromwellApiClient
-          databaseMigration
-          databaseSql
-          dockerHashing
-          drsFileSystem
-          engine
-          ftpFileSystem
-          gcsFileSystem
-          googlePipelinesCommon
-          googlePipelinesV2Alpha1
-          googlePipelinesV2Beta
-          httpFileSystem
-          languageFactoryCore
-          perf
-          root
-          server
-          services
-          sfsBackend
-          sraFileSystem
-          tesBackend
-          wdlBiscayneLanguageFactory
-          wdlDraft2LanguageFactory
-          wdlDraft3LanguageFactory
-          wdlModelBiscayne
-          wdlModelDraft2
-          wdlModelDraft3
-          wdlNewBaseTransforms
-          wdlSharedModel
-          wdlSharedTransforms
-          wdlTransformsBiscayne
-          wdlTransformsDraft2
-          wdlTransformsDraft3
-          wes2cromwell
-          wom
-          womtool]
+        sbtSubProject: [awsBackend,
+        awsS3FileSystem,
+        azureBlobFileSystem,
+        backend,
+        centaur,
+        cloud-nio-impl-drs,
+        cloud-nio-impl-ftp,
+        cloud-nio-spi,
+        cloud-nio-util,
+        cloudSupport,
+        common,
+        core,
+        cromiam,
+        cromwell-drs-localizer,
+        cromwellApiClient,
+        databaseMigration,
+        databaseSql,
+        dockerHashing,
+        drsFileSystem,
+        engine,
+        ftpFileSystem,
+        gcsFileSystem,
+        googlePipelinesCommon,
+        googlePipelinesV2Alpha1,
+        googlePipelinesV2Beta,
+        httpFileSystem,
+        languageFactoryCore,
+        perf,
+        server,
+        services,
+        sfsBackend,
+        sraFileSystem,
+        tesBackend,
+        wdlBiscayneLanguageFactory,
+        wdlDraft2LanguageFactory,
+        wdlDraft3LanguageFactory,
+        wdlModelBiscayne,
+        wdlModelDraft2,
+        wdlModelDraft3,
+        wdlNewBaseTransforms,
+        wdlSharedModel,
+        wdlSharedTransforms,
+        wdlTransformsBiscayne,
+        wdlTransformsDraft2,
+        wdlTransformsDraft3,
+        wes2cromwell,
+        wom,
+        womtool]
 
     #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest

From 05ff151b42385c9516eb5752c707813b3e3c85e1 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 13:14:52 -0500
Subject: [PATCH 130/213] commento

---
 .github/workflows/cromwell_unit_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index ed704e960be..a27c4051575 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -73,8 +73,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3 # required first to checkout the repo
-    - uses: ./.github/set_up_cromwell_action
+    - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
   

From 4e338c40d47376127b2b32c9808ed2c12319eec7 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 13:17:21 -0500
Subject: [PATCH 131/213] eof

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index a27c4051575..07cd26ef33a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -82,4 +82,4 @@ jobs:
     - name: Run tests
       run: |
         set -e
-        sbt "${{ matrix.sbtSubProject }}/test"
\ No newline at end of file
+        sbt "${{ matrix.sbtSubProject }}/test"

From 58e8f80ab7bf41109179b38aa8186803556af97f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 13:35:41 -0500
Subject: [PATCH 132/213] length

---
 .github/workflows/cromwell_unit_tests.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 07cd26ef33a..ff0eacd48b4 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -19,7 +19,7 @@ jobs:
   build-and-test: 
     strategy:
       fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
-      matrix: #this array is the output of the command `sbt projects` from the cromwell root directory, minus a bunch of superflous formatting that sbt adds.
+      matrix: #this array is the output of the command `sbt projects` from the cromwell root directory (minus lots of formatting)
         sbtSubProject: [awsBackend,
         awsS3FileSystem,
         azureBlobFileSystem,
@@ -69,7 +69,8 @@ jobs:
         wom,
         womtool]
 
-    #This action is using a Github free runner, rather than a Broad self-hosted one. This is because the Broad ones don't have sbt installed by default.
+    #This action is using a Github free runner, rather than a Broad self-hosted one.
+    #This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
 
     steps:

From 13b0062f7bee0b9e4cdef7588eac8dc48c2e5ac6 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 14:41:11 -0500
Subject: [PATCH 133/213] speedtest without cache

---
 .github/set_up_cromwell_action/action.yml | 2 +-
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 038aa2b0346..46a67870f4d 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -44,4 +44,4 @@ runs:
         with:
           distribution: temurin
           java-version: 11
-          cache: sbt
+          #cache: sbt
diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index ff0eacd48b4..0dbb40fc7fe 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -70,7 +70,7 @@ jobs:
         womtool]
 
     #This action is using a Github free runner, rather than a Broad self-hosted one.
-    #This is because the Broad ones don't have sbt installed by default.
+    This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
 
     steps:

From d9da2ed6631add2b1ad570a5e768e22b213a7f03 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 14:42:50 -0500
Subject: [PATCH 134/213] cacheless speedtest

---
 .github/set_up_cromwell_action/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 46a67870f4d..13cb11601db 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -44,4 +44,4 @@ runs:
         with:
           distribution: temurin
           java-version: 11
-          #cache: sbt
+

From e00aad3f17e39958c9553293123df1fddab5af17 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 14:44:33 -0500
Subject: [PATCH 135/213] kids call these things hashtags

---
 .github/workflows/cromwell_unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 0dbb40fc7fe..ff0eacd48b4 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -70,7 +70,7 @@ jobs:
         womtool]
 
     #This action is using a Github free runner, rather than a Broad self-hosted one.
-    This is because the Broad ones don't have sbt installed by default.
+    #This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
 
     steps:

From 83b8dafdc3faafefb6823e811211737acd435a68 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 31 Jan 2023 14:55:19 -0500
Subject: [PATCH 136/213] address PR feedback with liberal use of the delete
 key

---
 .github/workflows/cromwell_unit_tests.yml | 55 +----------------------
 1 file changed, 1 insertion(+), 54 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index ff0eacd48b4..122a40d1e1a 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -10,65 +10,12 @@ run-name: ${{ github.actor }} running Cromwell sbt unit tests.
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
   push:
-  pull_request: 
 
 permissions: 
   contents: read
 
 jobs:
   build-and-test: 
-    strategy:
-      fail-fast: false #Disabling fail fast means that even if one job in the matrix fails, the others will still try to complete.
-      matrix: #this array is the output of the command `sbt projects` from the cromwell root directory (minus lots of formatting)
-        sbtSubProject: [awsBackend,
-        awsS3FileSystem,
-        azureBlobFileSystem,
-        backend,
-        centaur,
-        cloud-nio-impl-drs,
-        cloud-nio-impl-ftp,
-        cloud-nio-spi,
-        cloud-nio-util,
-        cloudSupport,
-        common,
-        core,
-        cromiam,
-        cromwell-drs-localizer,
-        cromwellApiClient,
-        databaseMigration,
-        databaseSql,
-        dockerHashing,
-        drsFileSystem,
-        engine,
-        ftpFileSystem,
-        gcsFileSystem,
-        googlePipelinesCommon,
-        googlePipelinesV2Alpha1,
-        googlePipelinesV2Beta,
-        httpFileSystem,
-        languageFactoryCore,
-        perf,
-        server,
-        services,
-        sfsBackend,
-        sraFileSystem,
-        tesBackend,
-        wdlBiscayneLanguageFactory,
-        wdlDraft2LanguageFactory,
-        wdlDraft3LanguageFactory,
-        wdlModelBiscayne,
-        wdlModelDraft2,
-        wdlModelDraft3,
-        wdlNewBaseTransforms,
-        wdlSharedModel,
-        wdlSharedTransforms,
-        wdlTransformsBiscayne,
-        wdlTransformsDraft2,
-        wdlTransformsDraft3,
-        wes2cromwell,
-        wom,
-        womtool]
-
     #This action is using a Github free runner, rather than a Broad self-hosted one.
     #This is because the Broad ones don't have sbt installed by default.
     runs-on: ubuntu-latest
@@ -83,4 +30,4 @@ jobs:
     - name: Run tests
       run: |
         set -e
-        sbt "${{ matrix.sbtSubProject }}/test"
+        sbt "test"

From 4bc0bc89597352178dfa320727ac59b68980eefc Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 1 Feb 2023 09:17:34 -0500
Subject: [PATCH 137/213] fix up some comment

---
 .github/workflows/cromwell_unit_tests.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 122a40d1e1a..d0927f8b954 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -1,7 +1,6 @@
 name: 'Cromwell unit tests'
 
 #This github action runs all of Cromwell's unit tests.
-#A matrix strategy is used so that each subproject can be unit tested in parallel with all other subprojects. 
 
 #This is what shows up in the github workflows page as the title. 
 run-name: ${{ github.actor }} running Cromwell sbt unit tests.
@@ -26,7 +25,7 @@ jobs:
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
   
-    #Invoke SBT on a specific subproject, asking it to run all unit tests contained within that subproject.
+    #Invoke SBT to run all unit tests for Cromwell. 
     - name: Run tests
       run: |
         set -e

From 9d187373336c3f7e6677f6f8800edcc091409742 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 11:18:25 -0500
Subject: [PATCH 138/213] new yaml

---
 .github/workflows/centaur_local_test.yml | 34 ++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/centaur_local_test.yml

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
new file mode 100644
index 00000000000..ebc328234d2
--- /dev/null
+++ b/.github/workflows/centaur_local_test.yml
@@ -0,0 +1,34 @@
+name: 'Centaur Integration Tests'
+
+#This github action runs all of Cromwell's unit tests.
+
+#This is what shows up in the github workflows page as the title. 
+run-name: ${{ github.actor }} running Centaur Integration Tests.
+
+#What will trigger the workflow to run. 
+on:
+  workflow_dispatch: #Manual trigger from GitHub UI
+  push:
+
+permissions: 
+  contents: read
+
+jobs:
+  build-and-test: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+  
+    #Invoke SBT to build a cromwell jar
+    - name: Compile Cromwell
+      run: |
+        sbt assembly
+
+    #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
+    - name: Find Cromwell Jar
+      run: |
+        echo find server/target/scala-2.13/*.jar
\ No newline at end of file

From 50853a2a0c5f380b3541d0b8d60e019d5e0a19f6 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 11:31:08 -0500
Subject: [PATCH 139/213] testing

---
 .github/workflows/centaur_local_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index ebc328234d2..b14ad9b220f 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -29,6 +29,6 @@ jobs:
         sbt assembly
 
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
-    - name: Find Cromwell Jar
+    - name: Launch Cromwell jar
       run: |
-        echo find server/target/scala-2.13/*.jar
\ No newline at end of file
+        java -jar "$(server/target/scala-2.13/*.jar -print -quit)" server
\ No newline at end of file

From 4103cab9988740a9a9f624a045394a3a50f046f4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 11:42:03 -0500
Subject: [PATCH 140/213] testing

---
 .github/workflows/centaur_local_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index b14ad9b220f..7578dbd9a3d 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -31,4 +31,4 @@ jobs:
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
     - name: Launch Cromwell jar
       run: |
-        java -jar "$(server/target/scala-2.13/*.jar -print -quit)" server
\ No newline at end of file
+        java -jar "$(server/target/scala-2.13/*.jar -print -quit)" server

From da3a5af3a1eb9c90826dc581e328afffeb2ba719 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 11:43:44 -0500
Subject: [PATCH 141/213] testing

---
 .github/workflows/centaur_local_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 7578dbd9a3d..039dec75107 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -31,4 +31,4 @@ jobs:
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
     - name: Launch Cromwell jar
       run: |
-        java -jar "$(server/target/scala-2.13/*.jar -print -quit)" server
+        java -jar "$(find server/target/scala-2.13/*.jar -print -quit)" server

From 048f05243da8437d2025d82b517ee49c3be37839 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 14:51:58 -0500
Subject: [PATCH 142/213] testCentaurLocal

---
 .github/workflows/centaur_local_test.yml | 29 ++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 039dec75107..f2936937f2f 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -28,7 +28,32 @@ jobs:
       run: |
         sbt assembly
 
+    #Start the database that cromwell depends on
+    #- name: Launch Docker MySQL Database
+    #  run: |
+    #    ./processes/release_processes/scripts/start_publish_mysql_docker.sh
+
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
-    - name: Launch Cromwell jar
+    - name: Run Integration Test
       run: |
-        java -jar "$(find server/target/scala-2.13/*.jar -print -quit)" server
+        exec "${CROMWELL_BUILD_SCRIPTS_DIRECTORY}/testCentaurLocal.sh"
+      env:
+        CROMWELL_BUILD_PROVIDER: GITHUB_ACTIONS
+        CROMWELL_BUILD_HOME_DIRECTORY: "$(pwd)"
+        CROMWELL_BUILD_ROOT_DIRECTORY: "$(pwd)"
+        CROMWELL_BUILD_LOG_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/target/ci/logs"
+        CROMWELL_BUILD_CROMWELL_LOG: "${CROMWELL_BUILD_LOG_DIRECTORY}/cromwell.log"
+        CROMWELL_BUILD_DOCKER_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/docker-compose"
+        CROMWELL_BUILD_SCRIPTS_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/bin"
+        CROMWELL_BUILD_RESOURCES_SOURCES: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/resources"
+        CROMWELL_BUILD_RESOURCES_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/target/ci/resources"
+        CROMWELL_BUILD_GIT_SECRETS_DIRECTORY: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/git-secrets"
+        CROMWELL_BUILD_GIT_SECRETS_COMMIT: "ad82d68ee924906a0401dfd48de5057731a9bc84"
+        CROMWELL_BUILD_WAIT_FOR_IT_FILENAME: "wait-for-it.sh"
+        CROMWELL_BUILD_WAIT_FOR_IT_BRANCH: "db049716e42767d39961e95dd9696103dca813f1"
+        CROMWELL_BUILD_WAIT_FOR_IT_URL: "https://raw.githubusercontent.com/vishnubob/wait-for-it/${CROMWELL_BUILD_WAIT_FOR_IT_BRANCH}/${CROMWELL_BUILD_WAIT_FOR_IT_FILENAME}"
+        CROMWELL_BUILD_WAIT_FOR_IT_SCRIPT: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/${CROMWELL_BUILD_WAIT_FOR_IT_FILENAME}"
+        CROMWELL_BUILD_VAULT_ZIP: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/vault.zip"
+        CROMWELL_BUILD_VAULT_EXECUTABLE: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/vault"
+        CROMWELL_BUILD_EXIT_FUNCTIONS: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cromwell_build_exit_functions.$$"
+

From 684455e9a391cc55ab42b72c635efa7f2974f7c6 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 15:05:45 -0500
Subject: [PATCH 143/213] hardcodedpath

---
 .github/workflows/centaur_local_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index f2936937f2f..9247878302d 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -36,7 +36,7 @@ jobs:
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
     - name: Run Integration Test
       run: |
-        exec "${CROMWELL_BUILD_SCRIPTS_DIRECTORY}/testCentaurLocal.sh"
+        exec "./src/ci/bin/testCentaurLocal.sh"
       env:
         CROMWELL_BUILD_PROVIDER: GITHUB_ACTIONS
         CROMWELL_BUILD_HOME_DIRECTORY: "$(pwd)"

From 07e54f6c30869b89e275fc9ec66bfd69e7c915c2 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 15:06:25 -0500
Subject: [PATCH 144/213] testing

---
 .github/workflows/centaur_local_test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 9247878302d..89decca8c96 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -24,9 +24,9 @@ jobs:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
   
     #Invoke SBT to build a cromwell jar
-    - name: Compile Cromwell
-      run: |
-        sbt assembly
+    #- name: Compile Cromwell
+    #  run: |
+    #    sbt assembly
 
     #Start the database that cromwell depends on
     #- name: Launch Docker MySQL Database

From c76cb78e0d9df816bc1e505b555a6dc92a1cde3a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 15:17:59 -0500
Subject: [PATCH 145/213] testing

---
 .github/workflows/centaur_local_test.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 89decca8c96..d63d354c468 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -36,18 +36,18 @@ jobs:
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
     - name: Run Integration Test
       run: |
-        exec "./src/ci/bin/testCentaurLocal.sh"
+        exec "./src/ci/bin/test.sh"
       env:
         CROMWELL_BUILD_PROVIDER: GITHUB_ACTIONS
-        CROMWELL_BUILD_HOME_DIRECTORY: "$(pwd)"
-        CROMWELL_BUILD_ROOT_DIRECTORY: "$(pwd)"
-        CROMWELL_BUILD_LOG_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/target/ci/logs"
+        CROMWELL_BUILD_HOME_DIRECTORY: "."
+        CROMWELL_BUILD_ROOT_DIRECTORY: "."
+        CROMWELL_BUILD_LOG_DIRECTORY: "target/ci/logs"
         CROMWELL_BUILD_CROMWELL_LOG: "${CROMWELL_BUILD_LOG_DIRECTORY}/cromwell.log"
         CROMWELL_BUILD_DOCKER_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/docker-compose"
-        CROMWELL_BUILD_SCRIPTS_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/bin"
-        CROMWELL_BUILD_RESOURCES_SOURCES: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/resources"
-        CROMWELL_BUILD_RESOURCES_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/target/ci/resources"
-        CROMWELL_BUILD_GIT_SECRETS_DIRECTORY: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/git-secrets"
+        CROMWELL_BUILD_SCRIPTS_DIRECTORY: "src/ci/bin"
+        CROMWELL_BUILD_RESOURCES_SOURCES: "src/ci/resources"
+        CROMWELL_BUILD_RESOURCES_DIRECTORY: "target/ci/resources"
+        CROMWELL_BUILD_GIT_SECRETS_DIRECTORY: "target/ci/resources/git-secrets"
         CROMWELL_BUILD_GIT_SECRETS_COMMIT: "ad82d68ee924906a0401dfd48de5057731a9bc84"
         CROMWELL_BUILD_WAIT_FOR_IT_FILENAME: "wait-for-it.sh"
         CROMWELL_BUILD_WAIT_FOR_IT_BRANCH: "db049716e42767d39961e95dd9696103dca813f1"

From 1c14d290030b5eb3ad4392e74e495d4b5773b6fa Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 15:27:24 -0500
Subject: [PATCH 146/213] testing

---
 .github/workflows/centaur_local_test.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index d63d354c468..2d2de773b82 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -36,14 +36,16 @@ jobs:
     #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
     - name: Run Integration Test
       run: |
+        echo "${CROMWELL_BUILD_PROVIDER}"
+        echo "${CROMWELL_BUILD_HOME_DIRECTORY}"
         exec "./src/ci/bin/test.sh"
       env:
         CROMWELL_BUILD_PROVIDER: GITHUB_ACTIONS
         CROMWELL_BUILD_HOME_DIRECTORY: "."
         CROMWELL_BUILD_ROOT_DIRECTORY: "."
         CROMWELL_BUILD_LOG_DIRECTORY: "target/ci/logs"
-        CROMWELL_BUILD_CROMWELL_LOG: "${CROMWELL_BUILD_LOG_DIRECTORY}/cromwell.log"
-        CROMWELL_BUILD_DOCKER_DIRECTORY: "${CROMWELL_BUILD_ROOT_DIRECTORY}/src/ci/docker-compose"
+        CROMWELL_BUILD_CROMWELL_LOG: "target/ci/logs/cromwell.log"
+        CROMWELL_BUILD_DOCKER_DIRECTORY: "src/ci/docker-compose"
         CROMWELL_BUILD_SCRIPTS_DIRECTORY: "src/ci/bin"
         CROMWELL_BUILD_RESOURCES_SOURCES: "src/ci/resources"
         CROMWELL_BUILD_RESOURCES_DIRECTORY: "target/ci/resources"

From cd7da8cf552d2d2dc41d6fc1071659a15eba2f54 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 Feb 2023 15:49:36 -0500
Subject: [PATCH 147/213] testing

---
 .github/workflows/centaur_local_test.yml | 52 +++++-------------------
 1 file changed, 10 insertions(+), 42 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 2d2de773b82..5f1fbfd02fc 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -13,49 +13,17 @@ on:
 permissions: 
   contents: read
 
+env:
+  VAULT_TOKEN: ${{ secrets.VAULT_TOKEN }}
+
 jobs:
-  build-and-test: 
+  centaur-tests: 
+    env:
+      BUILD_NAME: centaurPapiUpgradePapiV2alpha1
+      BUILD_TYPE: centaurPapiUpgradePapiV2alpha1
+      BUILD_MYSQL: 5.7
     runs-on: ubuntu-latest
-
+    timeout-minutes: 120
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
-    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
-      with:
-        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
-  
-    #Invoke SBT to build a cromwell jar
-    #- name: Compile Cromwell
-    #  run: |
-    #    sbt assembly
-
-    #Start the database that cromwell depends on
-    #- name: Launch Docker MySQL Database
-    #  run: |
-    #    ./processes/release_processes/scripts/start_publish_mysql_docker.sh
-
-    #The name of the cromwell jar depends on its version number. Find the path to the jar we'd like to test
-    - name: Run Integration Test
-      run: |
-        echo "${CROMWELL_BUILD_PROVIDER}"
-        echo "${CROMWELL_BUILD_HOME_DIRECTORY}"
-        exec "./src/ci/bin/test.sh"
-      env:
-        CROMWELL_BUILD_PROVIDER: GITHUB_ACTIONS
-        CROMWELL_BUILD_HOME_DIRECTORY: "."
-        CROMWELL_BUILD_ROOT_DIRECTORY: "."
-        CROMWELL_BUILD_LOG_DIRECTORY: "target/ci/logs"
-        CROMWELL_BUILD_CROMWELL_LOG: "target/ci/logs/cromwell.log"
-        CROMWELL_BUILD_DOCKER_DIRECTORY: "src/ci/docker-compose"
-        CROMWELL_BUILD_SCRIPTS_DIRECTORY: "src/ci/bin"
-        CROMWELL_BUILD_RESOURCES_SOURCES: "src/ci/resources"
-        CROMWELL_BUILD_RESOURCES_DIRECTORY: "target/ci/resources"
-        CROMWELL_BUILD_GIT_SECRETS_DIRECTORY: "target/ci/resources/git-secrets"
-        CROMWELL_BUILD_GIT_SECRETS_COMMIT: "ad82d68ee924906a0401dfd48de5057731a9bc84"
-        CROMWELL_BUILD_WAIT_FOR_IT_FILENAME: "wait-for-it.sh"
-        CROMWELL_BUILD_WAIT_FOR_IT_BRANCH: "db049716e42767d39961e95dd9696103dca813f1"
-        CROMWELL_BUILD_WAIT_FOR_IT_URL: "https://raw.githubusercontent.com/vishnubob/wait-for-it/${CROMWELL_BUILD_WAIT_FOR_IT_BRANCH}/${CROMWELL_BUILD_WAIT_FOR_IT_FILENAME}"
-        CROMWELL_BUILD_WAIT_FOR_IT_SCRIPT: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/${CROMWELL_BUILD_WAIT_FOR_IT_FILENAME}"
-        CROMWELL_BUILD_VAULT_ZIP: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/vault.zip"
-        CROMWELL_BUILD_VAULT_EXECUTABLE: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/vault"
-        CROMWELL_BUILD_EXIT_FUNCTIONS: "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cromwell_build_exit_functions.$$"
-
+    - run: src/ci/bin/test.sh

From f0a10887041e32fe9f323ac7b2b18e45f54d21b2 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 12:46:11 -0500
Subject: [PATCH 148/213] testing

---
 .github/workflows/centaur_local_test.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 5f1fbfd02fc..3402ca2b3f9 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -13,9 +13,6 @@ on:
 permissions: 
   contents: read
 
-env:
-  VAULT_TOKEN: ${{ secrets.VAULT_TOKEN }}
-
 jobs:
   centaur-tests: 
     env:

From 9dac3d768560e5bd663ef646eaee9930131707f1 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 12:48:28 -0500
Subject: [PATCH 149/213] testing

---
 .github/workflows/centaur_local_test.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 3402ca2b3f9..bbffe4691a2 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -23,4 +23,6 @@ jobs:
     timeout-minutes: 120
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
-    - run: src/ci/bin/test.sh
+    - run: |
+      echo Running test.sh
+      ./src/ci/bin/test.sh

From 25ff7e60ebfb74179ab516254b6f1b4a82d67efa Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 12:50:03 -0500
Subject: [PATCH 150/213] testing

---
 .github/workflows/centaur_local_test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index bbffe4691a2..81c4977c123 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -25,4 +25,6 @@ jobs:
     - uses: actions/checkout@v3 # checkout the cromwell repo
     - run: |
       echo Running test.sh
+      echo $BUILD_NAME
+      echo $BUILD_TYPE
       ./src/ci/bin/test.sh

From 2e7b8796e947cbf26ab859bd04ea2d68df75b794 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 12:51:12 -0500
Subject: [PATCH 151/213] testing

---
 .github/workflows/centaur_local_test.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 81c4977c123..5c97db48fe2 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -24,7 +24,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
     - run: |
-      echo Running test.sh
-      echo $BUILD_NAME
-      echo $BUILD_TYPE
-      ./src/ci/bin/test.sh
+    echo Running test.sh
+    echo $BUILD_NAME
+    echo $BUILD_TYPE
+    ./src/ci/bin/test.sh

From 3b071bb13330bb49d543e08093b24c6b332d7958 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 12:53:07 -0500
Subject: [PATCH 152/213] syntax

---
 .github/workflows/centaur_local_test.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 5c97db48fe2..66c058b9f09 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -23,8 +23,9 @@ jobs:
     timeout-minutes: 120
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
-    - run: |
-    echo Running test.sh
-    echo $BUILD_NAME
-    echo $BUILD_TYPE
-    ./src/ci/bin/test.sh
+    - name: Run Centaur Test
+      run: |
+        echo Running test.sh
+        echo $BUILD_NAME
+        echo $BUILD_TYPE
+        ./src/ci/bin/test.sh

From b31b72ccfb5f5d121e7b2e619aee4ec3665a28b3 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 12:55:42 -0500
Subject: [PATCH 153/213] testing

---
 .github/workflows/centaur_local_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 66c058b9f09..c4d06935f96 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -25,7 +25,7 @@ jobs:
     - uses: actions/checkout@v3 # checkout the cromwell repo
     - name: Run Centaur Test
       run: |
+        set -e
         echo Running test.sh
         echo $BUILD_NAME
         echo $BUILD_TYPE
-        ./src/ci/bin/test.sh

From 30f3efb9bbaeddb9448e73f15bb889dffd4d8e63 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 13:40:22 -0500
Subject: [PATCH 154/213] testing

---
 .github/workflows/centaur_local_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index c4d06935f96..063367700f7 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -29,3 +29,4 @@ jobs:
         echo Running test.sh
         echo $BUILD_NAME
         echo $BUILD_TYPE
+        ls

From e6b095ba7e45fffcb363a68343dc1d0831999739 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 14:08:23 -0500
Subject: [PATCH 155/213] tesitng

---
 .github/workflows/centaur_local_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 063367700f7..423585f6933 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -29,4 +29,4 @@ jobs:
         echo Running test.sh
         echo $BUILD_NAME
         echo $BUILD_TYPE
-        ls
+        ./src/ci/bin/testSingleWorkflowRunner.sh

From 832adc3adb729431e3c0c6603fb898833e400708 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Feb 2023 14:11:54 -0500
Subject: [PATCH 156/213] tesitng

---
 .github/workflows/centaur_local_test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 423585f6933..23e59ad929d 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -23,6 +23,9 @@ jobs:
     timeout-minutes: 120
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
     - name: Run Centaur Test
       run: |
         set -e

From bc12969e26f93183ca90a755a6fd5d6762a97ceb Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Feb 2023 16:12:55 -0500
Subject: [PATCH 157/213] added github case

---
 src/ci/bin/test.inc.sh | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 95820513dfe..34429541a70 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -83,7 +83,9 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_PROVIDER_TRAVIS="travis"
     CROMWELL_BUILD_PROVIDER_JENKINS="jenkins"
     CROMWELL_BUILD_PROVIDER_CIRCLE="circle"
+    CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
+    echo setting environment variables
 
     if [[ "${TRAVIS-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_TRAVIS}"
@@ -91,6 +93,8 @@ cromwell::private::create_build_variables() {
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_JENKINS}"
     elif [[ "${CIRCLECI-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_CIRCLE}"
+    elif [[ "${GITHUB_ACTIONS-false}" == "true" ]]; then
+        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_GITHUB}"
     else
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_UNKNOWN}"
     fi
@@ -300,6 +304,22 @@ cromwell::private::create_build_variables() {
                 CROMWELL_BUILD_RUN_TESTS=true
             fi
             ;;
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
+            CROMWELL_BUILD_IS_CI=true
+            CROMWELL_BUILD_IS_SECURE=true
+            echo githubSpecific
+
+            CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
+            CROMWELL_BUILD_BRANCH="test-build-branch-string"
+            CROMWELL_BUILD_EVENT="test-build-event-string"
+            CROMWELL_BUILD_TAG="test-build-tag-string"
+            CROMWELL_BUILD_NUMBER="test-build-number-string"
+            CROMWELL_BUILD_URL="www.testBuildURL.com"
+            CROMWELL_BUILD_GIT_USER_EMAIL="testGitEmail"
+            CROMWELL_BUILD_GIT_USER_NAME="testGitUsername"
+            CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
+            CROMWELL_BUILD_GENERATE_COVERAGE=true
+            ;;
         *)
             CROMWELL_BUILD_IS_CI=false
             CROMWELL_BUILD_IS_SECURE=true

From bbde442089b8965d377a5f7b2b99d64f7a23df21 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Feb 2023 16:18:49 -0500
Subject: [PATCH 158/213] testing

---
 .github/workflows/centaur_local_test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 23e59ad929d..23980475cfd 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -16,8 +16,8 @@ permissions:
 jobs:
   centaur-tests: 
     env:
-      BUILD_NAME: centaurPapiUpgradePapiV2alpha1
-      BUILD_TYPE: centaurPapiUpgradePapiV2alpha1
+      BUILD_NAME: singleWorkflowRunner
+      BUILD_TYPE: singleWorkflowRunner
       BUILD_MYSQL: 5.7
     runs-on: ubuntu-latest
     timeout-minutes: 120
@@ -32,4 +32,4 @@ jobs:
         echo Running test.sh
         echo $BUILD_NAME
         echo $BUILD_TYPE
-        ./src/ci/bin/testSingleWorkflowRunner.sh
+        ./src/ci/bin/test.sh

From 83e39b36f6739d34263696276f8c0be4519e85fd Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Feb 2023 16:21:06 -0500
Subject: [PATCH 159/213] testing

---
 src/ci/bin/test.inc.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 34429541a70..2b135242852 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -319,6 +319,7 @@ cromwell::private::create_build_variables() {
             CROMWELL_BUILD_GIT_USER_NAME="testGitUsername"
             CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
             CROMWELL_BUILD_GENERATE_COVERAGE=true
+            CROMWELL_BUILD_RUN_TESTS=true
             ;;
         *)
             CROMWELL_BUILD_IS_CI=false

From b42b36bb94a1a8dd1fa5fb713c91494184841ae4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Feb 2023 16:26:47 -0500
Subject: [PATCH 160/213] testing

---
 src/ci/bin/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ci/bin/test.sh b/src/ci/bin/test.sh
index d148b1f808c..1e203e56840 100755
--- a/src/ci/bin/test.sh
+++ b/src/ci/bin/test.sh
@@ -4,5 +4,5 @@ set -o errexit -o nounset -o pipefail
 # import in shellcheck / CI / IntelliJ compatible ways
 # shellcheck source=/dev/null
 source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
+echo "in the root script"
 cromwell::build::exec_test_script

From 15accf963afa963087253e08891daec2f6d5004b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Feb 2023 16:31:02 -0500
Subject: [PATCH 161/213] testing

---
 src/ci/bin/testSingleWorkflowRunner.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/ci/bin/testSingleWorkflowRunner.sh b/src/ci/bin/testSingleWorkflowRunner.sh
index fcf0f626822..7a13cc90cd6 100755
--- a/src/ci/bin/testSingleWorkflowRunner.sh
+++ b/src/ci/bin/testSingleWorkflowRunner.sh
@@ -5,10 +5,13 @@ set -o errexit -o nounset -o pipefail +x
 # shellcheck source=/dev/null
 source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
 
+echo "about to set up common environment"
 cromwell::build::setup_common_environment
 
+echo "about to assemble jars"
 cromwell::build::assemble_jars
 
+echo "running java command"
 # Test 1: basic hello world
 java \
     -jar "${CROMWELL_BUILD_CROMWELL_JAR}" \

From 6ab676ef6d1e0a06bc8fbb1b93613dd3acbc693e Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Feb 2023 16:46:47 -0500
Subject: [PATCH 162/213] testing

---
 src/ci/bin/test.inc.sh | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 2b135242852..e2dee21cef6 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -85,7 +85,7 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_PROVIDER_CIRCLE="circle"
     CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
-    echo setting environment variables
+    echo "setting environment variables"
 
     if [[ "${TRAVIS-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_TRAVIS}"
@@ -307,7 +307,7 @@ cromwell::private::create_build_variables() {
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_IS_CI=true
             CROMWELL_BUILD_IS_SECURE=true
-            echo githubSpecific
+            echo "githubSpecific"
 
             CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
             CROMWELL_BUILD_BRANCH="test-build-branch-string"
@@ -1457,6 +1457,21 @@ cromwell::build::setup_common_environment() {
             cromwell::private::setup_pyenv_python_latest
             cromwell::private::start_docker_databases
             ;;
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
+            cromwell::private::stop_travis_defaults
+            # Try to login to vault, and if successful then use vault creds to login to docker.
+            # For those committers with vault access this avoids pull rate limits reported in BT-143.
+            cromwell::private::install_vault
+            cromwell::private::login_vault
+            cromwell::private::login_docker
+            cromwell::private::install_adoptopenjdk
+            cromwell::private::install_sbt_launcher
+            cromwell::private::install_docker_compose
+            cromwell::private::delete_boto_config
+            cromwell::private::delete_sbt_boot
+            cromwell::private::upgrade_pip
+            cromwell::private::start_docker_databases
+            ;;
         "${CROMWELL_BUILD_PROVIDER_JENKINS}"|\
         *)
             ;;

From 25145754771b6d75e514673cf97b3fc73bb6410b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 13:54:02 -0500
Subject: [PATCH 163/213] updated gitignore

---
 .gitignore | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.gitignore b/.gitignore
index 571a12c5873..35e8e4f9301 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,6 +17,12 @@ tags
 target
 /site
 
+#from running tests
+actual.json
+console_output.txt
+expected.json
+run_mode_metadata.json
+
 # custom config
 cromwell-executions
 cromwell-test-executions

From adcee04ae99fdbf26fb13f8aa8a99ab8feaecf90 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 14:02:00 -0500
Subject: [PATCH 164/213] testing

---
 src/ci/bin/test.inc.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index e2dee21cef6..ca747d3dc8d 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1457,7 +1457,7 @@ cromwell::build::setup_common_environment() {
             cromwell::private::setup_pyenv_python_latest
             cromwell::private::start_docker_databases
             ;;
-        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
+        "${CROMWELL_BUILD_PROVIDER_GITHUBg}")
             cromwell::private::stop_travis_defaults
             # Try to login to vault, and if successful then use vault creds to login to docker.
             # For those committers with vault access this avoids pull rate limits reported in BT-143.
@@ -1479,6 +1479,7 @@ cromwell::build::setup_common_environment() {
 
     cromwell::private::setup_secure_resources
     cromwell::private::start_build_heartbeat
+    echo "end of setup common environment"
 }
 
 

From 10b87e8982156fb1e220f403abf4925cb62f49ea Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 14:05:09 -0500
Subject: [PATCH 165/213] testing

---
 src/ci/bin/test.inc.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index ca747d3dc8d..7adf173b936 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -470,6 +470,7 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_WAIT_FOR_IT_FILENAME
     export CROMWELL_BUILD_WAIT_FOR_IT_SCRIPT
     export CROMWELL_BUILD_WAIT_FOR_IT_URL
+    echo "end creating build varaibles"
 }
 
 cromwell::private::echo_build_variables() {

From f2e6e9c596ae2abed1627f394c18a7a9155e56c3 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 14:07:42 -0500
Subject: [PATCH 166/213] testing

---
 src/ci/bin/test.inc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 7adf173b936..c0940319d15 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1458,7 +1458,7 @@ cromwell::build::setup_common_environment() {
             cromwell::private::setup_pyenv_python_latest
             cromwell::private::start_docker_databases
             ;;
-        "${CROMWELL_BUILD_PROVIDER_GITHUBg}")
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             cromwell::private::stop_travis_defaults
             # Try to login to vault, and if successful then use vault creds to login to docker.
             # For those committers with vault access this avoids pull rate limits reported in BT-143.

From 27601ca8b386534eb22395ffe06c3d4572405886 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 14:24:47 -0500
Subject: [PATCH 167/213] testing

---
 src/ci/bin/test.inc.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index c0940319d15..8039595ab2a 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -898,6 +898,7 @@ cromwell::private::install_vault() {
         --output "${CROMWELL_BUILD_VAULT_ZIP}" \
         "https://releases.hashicorp.com/vault/1.6.3/vault_1.6.3_${CROMWELL_BUILD_OS}_amd64.zip"
     unzip "${CROMWELL_BUILD_VAULT_ZIP}" -d "$(dirname "${CROMWELL_BUILD_VAULT_EXECUTABLE}")"
+    echo "Installed Vault"
 }
 
 cromwell::private::install_git_secrets() {

From 2d2b45f3ec9d6f5f7cc0781b5735b5f993513009 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 15:51:31 -0500
Subject: [PATCH 168/213] testing

---
 .github/workflows/centaur_local_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 23980475cfd..18d4d642561 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -19,6 +19,7 @@ jobs:
       BUILD_NAME: singleWorkflowRunner
       BUILD_TYPE: singleWorkflowRunner
       BUILD_MYSQL: 5.7
+      VAULT_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
     runs-on: ubuntu-latest
     timeout-minutes: 120
     steps:

From a78cfb29db6bc23d9f7de746ecb4bfeca96077b4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 7 Feb 2023 16:08:58 -0500
Subject: [PATCH 169/213] testing

---
 src/ci/bin/test.inc.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 8039595ab2a..da22f91c8c8 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1084,8 +1084,10 @@ cromwell::private::login_vault() {
                     write -field=token \
                     auth/approle/login role_id="${VAULT_ROLE_ID}" secret_id="${VAULT_SECRET_ID}"
             )"
+            echo "Trying to login to vault"
         else
             vault_token="${VAULT_TOKEN:-}"
+            echo "Using Env Vault Token"
         fi
 
         if [[ -n "${vault_token}" ]]; then
@@ -1095,6 +1097,7 @@ cromwell::private::login_vault() {
                 login "${vault_token}" < /dev/null > /dev/null \
                 && echo vault login success \
                 || true
+            echo "Vault login"
         fi
     fi
 }

From 42427ace7c1e198b5261b7b834e587c8f2409900 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 13:57:07 -0500
Subject: [PATCH 170/213] testing

---
 .github/workflows/centaur_local_test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 18d4d642561..daf5e97cde3 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -20,6 +20,8 @@ jobs:
       BUILD_TYPE: singleWorkflowRunner
       BUILD_MYSQL: 5.7
       VAULT_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+      VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
+      VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest
     timeout-minutes: 120
     steps:

From 947d2dc45b7c99b935f77c87cee7f2254810a746 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:01:07 -0500
Subject: [PATCH 171/213] testing

---
 .github/workflows/centaur_local_test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index daf5e97cde3..4a4936945dd 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -19,7 +19,6 @@ jobs:
       BUILD_NAME: singleWorkflowRunner
       BUILD_TYPE: singleWorkflowRunner
       BUILD_MYSQL: 5.7
-      VAULT_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest

From 540649240a2655f8b9e4c972dcdb92c5d2d1370a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:16:58 -0500
Subject: [PATCH 172/213] remove java

---
 .github/set_up_cromwell_action/action.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 13cb11601db..b12d3e82d94 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -39,9 +39,9 @@ runs:
           token: ${{ inputs.cromwell_repo_token }}
 
       #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
-      - name: Setup JDK
-        uses: actions/setup-java@v3
-        with:
-          distribution: temurin
-          java-version: 11
+      #- name: Setup JDK
+      #  uses: actions/setup-java@v3
+      #  with:
+      #    distribution: temurin
+      #    java-version: 11
 

From 7f53170d678a27c3561a37a0b77c1cf4c62947c0 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:21:52 -0500
Subject: [PATCH 173/213] testing

---
 .github/set_up_cromwell_action/action.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index b12d3e82d94..514e8a62db6 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -10,10 +10,10 @@ runs:
   using: "composite" # <-- this allows these steps to be used by other workflows.
   steps:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
-      - uses: actions/checkout@v3
-        name: Checkout Coursier Cache
-      - uses: coursier/cache-action@v6  
-        name: Enable Coursier Cache
+      #- uses: actions/checkout@v3
+      #  name: Checkout Coursier Cache
+      #- uses: coursier/cache-action@v6  
+      #  name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 

From f094e2b879f0c82c4db67171fb42e8e158448231 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:31:36 -0500
Subject: [PATCH 174/213] testing

---
 src/ci/bin/test.inc.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index da22f91c8c8..4e9b51ce9da 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -835,8 +835,11 @@ cromwell::private::install_adoptopenjdk() {
             grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
         ) main" |
         sudo tee /etc/apt/sources.list.d/adoptopenjdk.list
+    echo "before update"
     sudo apt-get update
+    echo "before get install"
     sudo apt-get install -y adoptopenjdk-11-hotspot
+    echo "before alternatives"
     sudo update-java-alternatives --set adoptopenjdk-11-hotspot-amd64
 }
 

From 2a3c41a95f9a16c1718e121bd750779ae72d7d44 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:35:03 -0500
Subject: [PATCH 175/213] testing

---
 src/ci/bin/test.inc.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 4e9b51ce9da..e3f1f5f2a5b 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -835,6 +835,7 @@ cromwell::private::install_adoptopenjdk() {
             grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
         ) main" |
         sudo tee /etc/apt/sources.list.d/adoptopenjdk.list
+    lsb_release -a
     echo "before update"
     sudo apt-get update
     echo "before get install"

From 50b92b55a60584f3266720dceb5c953f051f13fc Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:46:08 -0500
Subject: [PATCH 176/213] testing

---
 .github/set_up_cromwell_action/action.yml | 12 ++++++------
 src/ci/bin/test.inc.sh                    |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 514e8a62db6..d889a9c14bb 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -38,10 +38,10 @@ runs:
           repository: broadinstitute/cromwell
           token: ${{ inputs.cromwell_repo_token }}
 
-      #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
-      #- name: Setup JDK
-      #  uses: actions/setup-java@v3
-      #  with:
-      #    distribution: temurin
-      #    java-version: 11
+      Install Java to this VM. This Java version and distribution is compatible with Cromwell.
+      - name: Setup JDK
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
 
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index e3f1f5f2a5b..7c4e4949e4a 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1473,7 +1473,7 @@ cromwell::build::setup_common_environment() {
             cromwell::private::install_vault
             cromwell::private::login_vault
             cromwell::private::login_docker
-            cromwell::private::install_adoptopenjdk
+            #cromwell::private::install_adoptopenjdk
             cromwell::private::install_sbt_launcher
             cromwell::private::install_docker_compose
             cromwell::private::delete_boto_config

From d35e7885c090d8ef146d3418f22c1774b04cf992 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:48:29 -0500
Subject: [PATCH 177/213] testing

---
 .github/set_up_cromwell_action/action.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index d889a9c14bb..13cb11601db 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -10,10 +10,10 @@ runs:
   using: "composite" # <-- this allows these steps to be used by other workflows.
   steps:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
-      #- uses: actions/checkout@v3
-      #  name: Checkout Coursier Cache
-      #- uses: coursier/cache-action@v6  
-      #  name: Enable Coursier Cache
+      - uses: actions/checkout@v3
+        name: Checkout Coursier Cache
+      - uses: coursier/cache-action@v6  
+        name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 
@@ -38,7 +38,7 @@ runs:
           repository: broadinstitute/cromwell
           token: ${{ inputs.cromwell_repo_token }}
 
-      Install Java to this VM. This Java version and distribution is compatible with Cromwell.
+      #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
       - name: Setup JDK
         uses: actions/setup-java@v3
         with:

From c9674dcec0fd1f7f231f80d7dfcf733c3e5b3695 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 14:51:55 -0500
Subject: [PATCH 178/213] testing

---
 src/ci/bin/test.inc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 7c4e4949e4a..7981e93ef5a 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1474,7 +1474,7 @@ cromwell::build::setup_common_environment() {
             cromwell::private::login_vault
             cromwell::private::login_docker
             #cromwell::private::install_adoptopenjdk
-            cromwell::private::install_sbt_launcher
+            #cromwell::private::install_sbt_launcher
             cromwell::private::install_docker_compose
             cromwell::private::delete_boto_config
             cromwell::private::delete_sbt_boot

From 45d64f383331874b9a638cc1803ba42e51b91ef9 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 15:10:16 -0500
Subject: [PATCH 179/213] testing

---
 .github/workflows/centaur_local_test.yml | 4 ++--
 src/ci/bin/test.inc.sh                   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 4a4936945dd..295e701ba6f 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -16,8 +16,8 @@ permissions:
 jobs:
   centaur-tests: 
     env:
-      BUILD_NAME: singleWorkflowRunner
-      BUILD_TYPE: singleWorkflowRunner
+      BUILD_NAME: centaurPapiV2beta
+      BUILD_TYPE: centaurPapiV2beta
       BUILD_MYSQL: 5.7
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 7981e93ef5a..597efb39754 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1473,8 +1473,8 @@ cromwell::build::setup_common_environment() {
             cromwell::private::install_vault
             cromwell::private::login_vault
             cromwell::private::login_docker
-            #cromwell::private::install_adoptopenjdk
-            #cromwell::private::install_sbt_launcher
+            #Note: Unlike with other CI providers, we are using Github Actions to install Java and sbt for us.
+            #This is automatically handled in the set_up_cromwell Github Action, which can be found in [cromwell root]/.github/set_up_cromwell_aciton.
             cromwell::private::install_docker_compose
             cromwell::private::delete_boto_config
             cromwell::private::delete_sbt_boot

From a9327ea751b8b90794e536af678d1bd66179b3c5 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 15:54:20 -0500
Subject: [PATCH 180/213] testing

---
 .github/workflows/centaur_local_test.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 295e701ba6f..16f13f7c387 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -14,10 +14,14 @@ permissions:
   contents: read
 
 jobs:
-  centaur-tests: 
+  centaur-tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        build_type: [centaurPapiV2beta, testSingleWorkflowRunner, centaurLocal]
     env:
-      BUILD_NAME: centaurPapiV2beta
-      BUILD_TYPE: centaurPapiV2beta
+      BUILD_NAME: ${{ matrix.build_type }}
+      BUILD_TYPE: ${{ matrix.build_type }}
       BUILD_MYSQL: 5.7
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
@@ -32,6 +36,4 @@ jobs:
       run: |
         set -e
         echo Running test.sh
-        echo $BUILD_NAME
-        echo $BUILD_TYPE
         ./src/ci/bin/test.sh

From 7b3351c1ff81d238daa27eee78899716ce52d1e5 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 9 Feb 2023 15:57:47 -0500
Subject: [PATCH 181/213] spelling

---
 .github/workflows/centaur_local_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_local_test.yml
index 16f13f7c387..b0af584f655 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_local_test.yml
@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        build_type: [centaurPapiV2beta, testSingleWorkflowRunner, centaurLocal]
+        build_type: [centaurPapiV2beta, singleWorkflowRunner, centaurLocal]
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}

From 335104ab5ae3f21472c7ac79b71e3cf85a4fae04 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:37:03 -0500
Subject: [PATCH 182/213] testing

---
 ...taur_local_test.yml => centaur_integration_tests.yml} | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)
 rename .github/workflows/{centaur_local_test.yml => centaur_integration_tests.yml} (83%)

diff --git a/.github/workflows/centaur_local_test.yml b/.github/workflows/centaur_integration_tests.yml
similarity index 83%
rename from .github/workflows/centaur_local_test.yml
rename to .github/workflows/centaur_integration_tests.yml
index b0af584f655..c0fd27c3e20 100644
--- a/.github/workflows/centaur_local_test.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -18,11 +18,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        build_type: [centaurPapiV2beta, singleWorkflowRunner, centaurLocal]
+        include:
+          -build_type: centaurPapiV2Beta
+            build_mysql: 5.7
+          -build_type: dbms
+          -build_type: centaurTes
+            build_mysql: 5.7
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}
-      BUILD_MYSQL: 5.7
+      BUILD_MYSQL: matrix.build_mysql
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest

From 4c6e4ee7d852fcf6060c6b58299332c1fff19df7 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:38:00 -0500
Subject: [PATCH 183/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index c0fd27c3e20..771059a5a10 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -20,10 +20,10 @@ jobs:
       matrix:
         include:
           -build_type: centaurPapiV2Beta
-            build_mysql: 5.7
+          build_mysql: 5.7
           -build_type: dbms
           -build_type: centaurTes
-            build_mysql: 5.7
+          build_mysql: 5.7
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}

From a9f1bc7276d3b46ac0f94469442f69fa38b1926c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:39:51 -0500
Subject: [PATCH 184/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 771059a5a10..6993e2d705e 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -16,7 +16,6 @@ permissions:
 jobs:
   centaur-tests:
     strategy:
-      fail-fast: false
       matrix:
         include:
           -build_type: centaurPapiV2Beta

From 21de2ec84992700b15cc27ab2818e3f41826aa45 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:42:17 -0500
Subject: [PATCH 185/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 6993e2d705e..af4f0f8bca3 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -16,12 +16,13 @@ permissions:
 jobs:
   centaur-tests:
     strategy:
+      fail-fast: false
       matrix:
         include:
-          -build_type: centaurPapiV2Beta
+          - build_type: centaurPapiV2Beta
           build_mysql: 5.7
-          -build_type: dbms
-          -build_type: centaurTes
+          - build_type: dbms
+          - build_type: centaurTes
           build_mysql: 5.7
     env:
       BUILD_NAME: ${{ matrix.build_type }}

From 283d84b4b3df708ab856781f5f1d1cc938495540 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:43:37 -0500
Subject: [PATCH 186/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index af4f0f8bca3..b23d3d0f0ad 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -20,10 +20,10 @@ jobs:
       matrix:
         include:
           - build_type: centaurPapiV2Beta
-          build_mysql: 5.7
+            build_mysql: 5.7
           - build_type: dbms
           - build_type: centaurTes
-          build_mysql: 5.7
+            build_mysql: 5.7
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}

From 6e8a5d3b0c0a1eb33858abc881415792499d3116 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:46:39 -0500
Subject: [PATCH 187/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index b23d3d0f0ad..f354cb66294 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - build_type: centaurPapiV2Beta
+          - build_type: centaurPapiV2beta
             build_mysql: 5.7
           - build_type: dbms
           - build_type: centaurTes

From e6ff2274149e50b66f9caf3888a9a5950c2a8d69 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:49:41 -0500
Subject: [PATCH 188/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index f354cb66294..822c0680aa0 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -27,7 +27,7 @@ jobs:
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}
-      BUILD_MYSQL: matrix.build_mysql
+      BUILD_MYSQL: ${{ matrix.build_mysql }}
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest

From b8a6a0d890ecaad7f0e6636352e60bf7c1a609dd Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:52:54 -0500
Subject: [PATCH 189/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 822c0680aa0..7b9fe121d63 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -24,10 +24,18 @@ jobs:
           - build_type: dbms
           - build_type: centaurTes
             build_mysql: 5.7
+          - build_type: centaurEngineUpgradeLocal
+          - build_type: centaurLocal
+            build_mysql: 5.7
+          - build_type: centaurLocal
+            build_postgresql: 11.3
+          - build_type: checkPublish
+
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}
       BUILD_MYSQL: ${{ matrix.build_mysql }}
+      BUILD_POSTGRESQL: ${{ matrix.build_postgresql }}
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest

From 70e3701c09adcd5318f9ced9ad8a888f8c5d5071 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 13:58:21 -0500
Subject: [PATCH 190/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 7b9fe121d63..fedfc33bbd3 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -30,12 +30,25 @@ jobs:
           - build_type: centaurLocal
             build_postgresql: 11.3
           - build_type: checkPublish
-
+          - build_type: centaurAws
+            build_mysql: 5.7
+          - build_type: centaurDummy
+            build_mysql: 5.7
+          - build_type: centaurHoricromtalPapiV2beta
+            build_mysql: 5.7
+          - build_type: centaurSlurm
+            build_mysql: 5.7
+          - build_type: horicromtalDeadlock
+          - build_type: singleWorkflowRunner
+          - build_type: referenceDiskManifestBuilderApp
+          - build_type: centaurLocal
+            build_mariadb: 10.3
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }}
       BUILD_MYSQL: ${{ matrix.build_mysql }}
       BUILD_POSTGRESQL: ${{ matrix.build_postgresql }}
+      BUILD_MATRIADB: ${{ matrix.build_mariadb }}
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest

From 591c55aa13f48d5a8989b1e158f664454dfde589 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 14:16:05 -0500
Subject: [PATCH 191/213] testing

---
 src/ci/bin/test.inc.sh | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 597efb39754..aefe9a2019a 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -85,7 +85,6 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_PROVIDER_CIRCLE="circle"
     CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
-    echo "setting environment variables"
 
     if [[ "${TRAVIS-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_TRAVIS}"
@@ -310,13 +309,13 @@ cromwell::private::create_build_variables() {
             echo "githubSpecific"
 
             CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
-            CROMWELL_BUILD_BRANCH="test-build-branch-string"
-            CROMWELL_BUILD_EVENT="test-build-event-string"
-            CROMWELL_BUILD_TAG="test-build-tag-string"
-            CROMWELL_BUILD_NUMBER="test-build-number-string"
-            CROMWELL_BUILD_URL="www.testBuildURL.com"
-            CROMWELL_BUILD_GIT_USER_EMAIL="testGitEmail"
-            CROMWELL_BUILD_GIT_USER_NAME="testGitUsername"
+            CROMWELL_BUILD_BRANCH="${GITHUB_REF_NAME}"
+            CROMWELL_BUILD_EVENT="${GITHUB_EVENT_NAME}"
+            CROMWELL_BUILD_TAG=""
+            CROMWELL_BUILD_NUMBER="${GITHUB_RUN_ID}"
+            CROMWELL_BUILD_URL="${$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID}"
+            CROMWELL_BUILD_GIT_USER_EMAIL=""
+            CROMWELL_BUILD_GIT_USER_NAME="${GITHUB_ACTOR}"
             CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
             CROMWELL_BUILD_GENERATE_COVERAGE=true
             CROMWELL_BUILD_RUN_TESTS=true

From d8ba52976fcffcf35059d603e7beca81f8f1ab03 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 14:18:00 -0500
Subject: [PATCH 192/213] testing

---
 src/ci/bin/test.inc.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index aefe9a2019a..4ccaa97bf8b 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -313,7 +313,7 @@ cromwell::private::create_build_variables() {
             CROMWELL_BUILD_EVENT="${GITHUB_EVENT_NAME}"
             CROMWELL_BUILD_TAG=""
             CROMWELL_BUILD_NUMBER="${GITHUB_RUN_ID}"
-            CROMWELL_BUILD_URL="${$GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID}"
+            CROMWELL_BUILD_URL="${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
             CROMWELL_BUILD_GIT_USER_EMAIL=""
             CROMWELL_BUILD_GIT_USER_NAME="${GITHUB_ACTOR}"
             CROMWELL_BUILD_HEARTBEAT_PATTERN="…"

From eb2552240d3fd4bf7a299330381e397f8c40d8dd Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 14:25:42 -0500
Subject: [PATCH 193/213] cleanup

---
 src/ci/bin/test.inc.sh                 | 15 ++-------------
 src/ci/bin/test.sh                     |  1 -
 src/ci/bin/testSingleWorkflowRunner.sh |  3 ---
 3 files changed, 2 insertions(+), 17 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 4ccaa97bf8b..19e564159fb 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -306,8 +306,6 @@ cromwell::private::create_build_variables() {
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_IS_CI=true
             CROMWELL_BUILD_IS_SECURE=true
-            echo "githubSpecific"
-
             CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
             CROMWELL_BUILD_BRANCH="${GITHUB_REF_NAME}"
             CROMWELL_BUILD_EVENT="${GITHUB_EVENT_NAME}"
@@ -469,7 +467,6 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_WAIT_FOR_IT_FILENAME
     export CROMWELL_BUILD_WAIT_FOR_IT_SCRIPT
     export CROMWELL_BUILD_WAIT_FOR_IT_URL
-    echo "end creating build varaibles"
 }
 
 cromwell::private::echo_build_variables() {
@@ -834,12 +831,8 @@ cromwell::private::install_adoptopenjdk() {
             grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
         ) main" |
         sudo tee /etc/apt/sources.list.d/adoptopenjdk.list
-    lsb_release -a
-    echo "before update"
     sudo apt-get update
-    echo "before get install"
     sudo apt-get install -y adoptopenjdk-11-hotspot
-    echo "before alternatives"
     sudo update-java-alternatives --set adoptopenjdk-11-hotspot-amd64
 }
 
@@ -901,7 +894,6 @@ cromwell::private::install_vault() {
         --output "${CROMWELL_BUILD_VAULT_ZIP}" \
         "https://releases.hashicorp.com/vault/1.6.3/vault_1.6.3_${CROMWELL_BUILD_OS}_amd64.zip"
     unzip "${CROMWELL_BUILD_VAULT_ZIP}" -d "$(dirname "${CROMWELL_BUILD_VAULT_EXECUTABLE}")"
-    echo "Installed Vault"
 }
 
 cromwell::private::install_git_secrets() {
@@ -1087,10 +1079,8 @@ cromwell::private::login_vault() {
                     write -field=token \
                     auth/approle/login role_id="${VAULT_ROLE_ID}" secret_id="${VAULT_SECRET_ID}"
             )"
-            echo "Trying to login to vault"
         else
             vault_token="${VAULT_TOKEN:-}"
-            echo "Using Env Vault Token"
         fi
 
         if [[ -n "${vault_token}" ]]; then
@@ -1100,7 +1090,6 @@ cromwell::private::login_vault() {
                 login "${vault_token}" < /dev/null > /dev/null \
                 && echo vault login success \
                 || true
-            echo "Vault login"
         fi
     fi
 }
@@ -1473,7 +1462,8 @@ cromwell::build::setup_common_environment() {
             cromwell::private::login_vault
             cromwell::private::login_docker
             #Note: Unlike with other CI providers, we are using Github Actions to install Java and sbt for us.
-            #This is automatically handled in the set_up_cromwell Github Action, which can be found in [cromwell root]/.github/set_up_cromwell_aciton.
+            #This is automatically handled in the set_up_cromwell Github Action, which can be found in
+            #[cromwell root]/.github/set_up_cromwell_aciton.
             cromwell::private::install_docker_compose
             cromwell::private::delete_boto_config
             cromwell::private::delete_sbt_boot
@@ -1487,7 +1477,6 @@ cromwell::build::setup_common_environment() {
 
     cromwell::private::setup_secure_resources
     cromwell::private::start_build_heartbeat
-    echo "end of setup common environment"
 }
 
 
diff --git a/src/ci/bin/test.sh b/src/ci/bin/test.sh
index 1e203e56840..1e576430e11 100755
--- a/src/ci/bin/test.sh
+++ b/src/ci/bin/test.sh
@@ -4,5 +4,4 @@ set -o errexit -o nounset -o pipefail
 # import in shellcheck / CI / IntelliJ compatible ways
 # shellcheck source=/dev/null
 source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-echo "in the root script"
 cromwell::build::exec_test_script
diff --git a/src/ci/bin/testSingleWorkflowRunner.sh b/src/ci/bin/testSingleWorkflowRunner.sh
index 7a13cc90cd6..fcf0f626822 100755
--- a/src/ci/bin/testSingleWorkflowRunner.sh
+++ b/src/ci/bin/testSingleWorkflowRunner.sh
@@ -5,13 +5,10 @@ set -o errexit -o nounset -o pipefail +x
 # shellcheck source=/dev/null
 source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
 
-echo "about to set up common environment"
 cromwell::build::setup_common_environment
 
-echo "about to assemble jars"
 cromwell::build::assemble_jars
 
-echo "running java command"
 # Test 1: basic hello world
 java \
     -jar "${CROMWELL_BUILD_CROMWELL_JAR}" \

From b4ea121998712e0e1cbf33a3728066710ac446ee Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 14:45:35 -0500
Subject: [PATCH 194/213] testing

---
 .gitignore             | 2 +-
 src/ci/bin/test.inc.sh | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 35e8e4f9301..a80b4a21713 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,7 +17,7 @@ tags
 target
 /site
 
-#from running tests
+#from running integration tests locally
 actual.json
 console_output.txt
 expected.json
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 19e564159fb..058f63cdacf 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -484,6 +484,10 @@ cromwell::private::echo_build_variables() {
     echo "CROMWELL_BUILD_PROVIDER='${CROMWELL_BUILD_PROVIDER}'"
     echo "CROMWELL_BUILD_OS='${CROMWELL_BUILD_OS}'"
     echo "CROMWELL_BUILD_URL='${CROMWELL_BUILD_URL}'"
+    echo "CROMWELL_BUILD_URL='${BUILD_POSTGRESQL}'"
+    echo "CROMWELL_BUILD_URL='${BUILD_MATRIADB}'"
+    echo "CROMWELL_BUILD_URL='${BUILD_MYSQL}'"
+
 }
 
 # Create environment variables used by the DatabaseTestKit and cromwell::private::create_centaur_variables()

From fee57ffdbfdb857dee3670223ab1fe04fe83801c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:07:07 -0500
Subject: [PATCH 195/213] comments

---
 .github/workflows/centaur_integration_tests.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index fedfc33bbd3..7271a076ea4 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -8,7 +8,7 @@ run-name: ${{ github.actor }} running Centaur Integration Tests.
 #What will trigger the workflow to run. 
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
-  push:
+  push: #git push
 
 permissions: 
   contents: read
@@ -16,7 +16,8 @@ permissions:
 jobs:
   centaur-tests:
     strategy:
-      fail-fast: false
+      fail-fast: false #disabling fail-fast means that even if one tests fail, the others will still try to complete.
+      #Each entry below is a single integration test that lives in /src/ci/bin/.
       matrix:
         include:
           - build_type: centaurPapiV2beta
@@ -55,9 +56,11 @@ jobs:
     timeout-minutes: 120
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
-    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
+    - uses: ./.github/set_up_cromwell_action #This github action will set up git-secrets, caching, java, and sbt.
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+    #This script bascially just looks up another script to exececute, assuming that the other script's filename is
+    #src/ci/bin/test${BUILD_TYPE}.sh
     - name: Run Centaur Test
       run: |
         set -e

From 8bbd7d2cb36706d62c827b43d65e03222cd4c402 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:09:59 -0500
Subject: [PATCH 196/213] testing

---
 src/ci/bin/test.inc.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 058f63cdacf..65092767c84 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -484,9 +484,9 @@ cromwell::private::echo_build_variables() {
     echo "CROMWELL_BUILD_PROVIDER='${CROMWELL_BUILD_PROVIDER}'"
     echo "CROMWELL_BUILD_OS='${CROMWELL_BUILD_OS}'"
     echo "CROMWELL_BUILD_URL='${CROMWELL_BUILD_URL}'"
-    echo "CROMWELL_BUILD_URL='${BUILD_POSTGRESQL}'"
-    echo "CROMWELL_BUILD_URL='${BUILD_MATRIADB}'"
-    echo "CROMWELL_BUILD_URL='${BUILD_MYSQL}'"
+    echo "BUILD_POSTGRESQL='${BUILD_POSTGRESQL}'"
+    echo "BUILD_MATRIADB='${BUILD_MATRIADB}'"
+    echo "BUILD_MYSQL='${BUILD_MYSQL}'"
 
 }
 

From a4e3c587d3b4da6ab6338e5aa5f9874a934f8d66 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:23:50 -0500
Subject: [PATCH 197/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 10 +++++-----
 src/ci/bin/test.inc.sh                          |  1 -
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 7271a076ea4..cbda155eaad 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -1,9 +1,9 @@
 name: 'Centaur Integration Tests'
 
-#This github action runs all of Cromwell's unit tests.
+#This github action runs all of Cromwell's integration tests.
 
 #This is what shows up in the github workflows page as the title. 
-run-name: ${{ github.actor }} running Centaur Integration Tests.
+run-name: ${{ github.actor }} Centaur Testing.
 
 #What will trigger the workflow to run. 
 on:
@@ -16,7 +16,7 @@ permissions:
 jobs:
   centaur-tests:
     strategy:
-      fail-fast: false #disabling fail-fast means that even if one tests fail, the others will still try to complete.
+      fail-fast: false #disabling fail-fast means that even if one test fails, the others will still try to complete.
       #Each entry below is a single integration test that lives in /src/ci/bin/.
       matrix:
         include:
@@ -59,8 +59,8 @@ jobs:
     - uses: ./.github/set_up_cromwell_action #This github action will set up git-secrets, caching, java, and sbt.
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
-    #This script bascially just looks up another script to exececute, assuming that the other script's filename is
-    #src/ci/bin/test${BUILD_TYPE}.sh
+    #This script bascially just looks up another script to run, assuming that the other script's filename is:
+    #src/ci/bin/test${BUILD_TYPE}.sh. The first letter of the BUILD_TYPE is automatically capitalized when looking for the filename.
     - name: Run Centaur Test
       run: |
         set -e
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 65092767c84..25aa8f33729 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1459,7 +1459,6 @@ cromwell::build::setup_common_environment() {
             cromwell::private::start_docker_databases
             ;;
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
-            cromwell::private::stop_travis_defaults
             # Try to login to vault, and if successful then use vault creds to login to docker.
             # For those committers with vault access this avoids pull rate limits reported in BT-143.
             cromwell::private::install_vault

From 6b25da0d19b2f885be9e3ece7bd71d7e7f50d60f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:24:21 -0500
Subject: [PATCH 198/213] whitespace

---
 src/ci/bin/test.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ci/bin/test.sh b/src/ci/bin/test.sh
index 1e576430e11..d148b1f808c 100755
--- a/src/ci/bin/test.sh
+++ b/src/ci/bin/test.sh
@@ -4,4 +4,5 @@ set -o errexit -o nounset -o pipefail
 # import in shellcheck / CI / IntelliJ compatible ways
 # shellcheck source=/dev/null
 source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
+
 cromwell::build::exec_test_script

From f9e712bb4b4febc5f61013a02bcb9efd2e934794 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:26:24 -0500
Subject: [PATCH 199/213] commento

---
 .github/workflows/centaur_integration_tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index cbda155eaad..2d7f59416e4 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -17,7 +17,8 @@ jobs:
   centaur-tests:
     strategy:
       fail-fast: false #disabling fail-fast means that even if one test fails, the others will still try to complete.
-      #Each entry below is a single integration test that lives in /src/ci/bin/.
+      #Each entry below is a single integration test that lives in /src/ci/bin/. 
+      #Each will be launched on its own runner so they can occur in parallel.
       matrix:
         include:
           - build_type: centaurPapiV2beta

From 90b0c7b1c4ef61b0cb91c855f690a9336b5503b2 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:28:54 -0500
Subject: [PATCH 200/213] commento

---
 .github/workflows/centaur_integration_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 2d7f59416e4..371aa3823da 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -47,7 +47,7 @@ jobs:
             build_mariadb: 10.3
     env:
       BUILD_NAME: ${{ matrix.build_type }}
-      BUILD_TYPE: ${{ matrix.build_type }}
+      BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable
       BUILD_MYSQL: ${{ matrix.build_mysql }}
       BUILD_POSTGRESQL: ${{ matrix.build_postgresql }}
       BUILD_MATRIADB: ${{ matrix.build_mariadb }}

From a3504d0fb3cbec8756530667ef1c4dc33f5d46df Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:31:58 -0500
Subject: [PATCH 201/213] testing

---
 .github/workflows/centaur_integration_tests.yml | 2 +-
 src/ci/bin/test.inc.sh                          | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 371aa3823da..9ce7c4c0202 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -61,7 +61,7 @@ jobs:
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
     #This script bascially just looks up another script to run, assuming that the other script's filename is:
-    #src/ci/bin/test${BUILD_TYPE}.sh. The first letter of the BUILD_TYPE is automatically capitalized when looking for the filename.
+    #src/ci/bin/test${BUILD_TYPE}.sh. The first letter of the BUILD_TYPE is automatically capitalized when looking.
     - name: Run Centaur Test
       run: |
         set -e
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 25aa8f33729..64965f7655a 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -487,7 +487,6 @@ cromwell::private::echo_build_variables() {
     echo "BUILD_POSTGRESQL='${BUILD_POSTGRESQL}'"
     echo "BUILD_MATRIADB='${BUILD_MATRIADB}'"
     echo "BUILD_MYSQL='${BUILD_MYSQL}'"
-
 }
 
 # Create environment variables used by the DatabaseTestKit and cromwell::private::create_centaur_variables()

From d51bdf8dca3bfcbb3616adf3cb6d8b78956a123b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 10 Feb 2023 15:44:29 -0500
Subject: [PATCH 202/213] testing

---
 src/ci/bin/test.inc.sh | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 64965f7655a..fe6d8cbbdd8 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -484,9 +484,6 @@ cromwell::private::echo_build_variables() {
     echo "CROMWELL_BUILD_PROVIDER='${CROMWELL_BUILD_PROVIDER}'"
     echo "CROMWELL_BUILD_OS='${CROMWELL_BUILD_OS}'"
     echo "CROMWELL_BUILD_URL='${CROMWELL_BUILD_URL}'"
-    echo "BUILD_POSTGRESQL='${BUILD_POSTGRESQL}'"
-    echo "BUILD_MATRIADB='${BUILD_MATRIADB}'"
-    echo "BUILD_MYSQL='${BUILD_MYSQL}'"
 }
 
 # Create environment variables used by the DatabaseTestKit and cromwell::private::create_centaur_variables()
@@ -497,7 +494,8 @@ cromwell::private::create_database_variables() {
 
     case "${CROMWELL_BUILD_PROVIDER}" in
         "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
+        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_MARIADB_HOSTNAME="localhost"
             CROMWELL_BUILD_MARIADB_PORT="23306"
             CROMWELL_BUILD_MARIADB_DOCKER_TAG="${BUILD_MARIADB-}"

From 032693a8f0e94bbf50df2d73764a2fd2ca466e98 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 10:03:19 -0500
Subject: [PATCH 203/213] these should pass

---
 .github/workflows/centaur_integration_tests.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/centaur_integration_tests.yml
index 9ce7c4c0202..9d1efa11bf9 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/centaur_integration_tests.yml
@@ -26,11 +26,8 @@ jobs:
           - build_type: dbms
           - build_type: centaurTes
             build_mysql: 5.7
-          - build_type: centaurEngineUpgradeLocal
           - build_type: centaurLocal
             build_mysql: 5.7
-          - build_type: centaurLocal
-            build_postgresql: 11.3
           - build_type: checkPublish
           - build_type: centaurAws
             build_mysql: 5.7
@@ -38,13 +35,8 @@ jobs:
             build_mysql: 5.7
           - build_type: centaurHoricromtalPapiV2beta
             build_mysql: 5.7
-          - build_type: centaurSlurm
-            build_mysql: 5.7
           - build_type: horicromtalDeadlock
           - build_type: singleWorkflowRunner
-          - build_type: referenceDiskManifestBuilderApp
-          - build_type: centaurLocal
-            build_mariadb: 10.3
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable

From 1454c3ffd53d435e1e555fcf6971caa1542ca2ce Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 14:18:16 -0500
Subject: [PATCH 204/213] testing PR comments

---
 ...ntaur_integration_tests.yml => integration_tests.yml} | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)
 rename .github/workflows/{centaur_integration_tests.yml => integration_tests.yml} (92%)

diff --git a/.github/workflows/centaur_integration_tests.yml b/.github/workflows/integration_tests.yml
similarity index 92%
rename from .github/workflows/centaur_integration_tests.yml
rename to .github/workflows/integration_tests.yml
index 9d1efa11bf9..ee32d1c0eb2 100644
--- a/.github/workflows/centaur_integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -1,9 +1,9 @@
-name: 'Centaur Integration Tests'
+name: 'Integration Tests'
 
 #This github action runs all of Cromwell's integration tests.
 
 #This is what shows up in the github workflows page as the title. 
-run-name: ${{ github.actor }} Centaur Testing.
+run-name: ${{ github.actor }} Integration Testing.
 
 #What will trigger the workflow to run. 
 on:
@@ -14,7 +14,7 @@ permissions:
   contents: read
 
 jobs:
-  centaur-tests:
+  integration-tests:
     strategy:
       fail-fast: false #disabling fail-fast means that even if one test fails, the others will still try to complete.
       #Each entry below is a single integration test that lives in /src/ci/bin/. 
@@ -23,6 +23,7 @@ jobs:
         include:
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
+            name: does this name work?
           - build_type: dbms
           - build_type: centaurTes
             build_mysql: 5.7
@@ -54,7 +55,7 @@ jobs:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
     #This script bascially just looks up another script to run, assuming that the other script's filename is:
     #src/ci/bin/test${BUILD_TYPE}.sh. The first letter of the BUILD_TYPE is automatically capitalized when looking.
-    - name: Run Centaur Test
+    - name: Run Integration Test
       run: |
         set -e
         echo Running test.sh

From 3356d8afec1c6cab2d65b69ab0550b92b0c399fa Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 14:21:01 -0500
Subject: [PATCH 205/213] remove unused name

---
 .github/workflows/integration_tests.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index ee32d1c0eb2..c9142508370 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -23,7 +23,6 @@ jobs:
         include:
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
-            name: does this name work?
           - build_type: dbms
           - build_type: centaurTes
             build_mysql: 5.7

From 2da0baeac1e1e80d48ea1effc7462de3a69782f2 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 14:33:28 -0500
Subject: [PATCH 206/213] testing name

---
 .github/workflows/integration_tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index c9142508370..085be4843a7 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -37,6 +37,7 @@ jobs:
             build_mysql: 5.7
           - build_type: horicromtalDeadlock
           - build_type: singleWorkflowRunner
+      name: ${{ matrix.build_type }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable

From dfcda981df8959641978bb48791b11955898cc79 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 14:34:33 -0500
Subject: [PATCH 207/213] naming

---
 .github/workflows/integration_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 085be4843a7..7fa445ef82e 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -37,7 +37,7 @@ jobs:
             build_mysql: 5.7
           - build_type: horicromtalDeadlock
           - build_type: singleWorkflowRunner
-      name: ${{ matrix.build_type }}
+    name: ${{ matrix.build_type }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable

From 8cd79e0ccd653deb073ec731d6721b4f2d0acbb0 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 14:38:14 -0500
Subject: [PATCH 208/213] Friendly Names

---
 .github/workflows/integration_tests.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 7fa445ef82e..0ea68b6050e 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -23,21 +23,30 @@ jobs:
         include:
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
+            friendly_name: Centaur Papi V2 Beta with MySQL 5.7
           - build_type: dbms
           - build_type: centaurTes
             build_mysql: 5.7
+            friendly_name: Centaur Tes with MySQL 5.7
           - build_type: centaurLocal
             build_mysql: 5.7
+            friendly_name: Centaur Local with MySQL 5.7
           - build_type: checkPublish
+            friendly_name: Check Publish
           - build_type: centaurAws
             build_mysql: 5.7
+            friendly_name: Centaur AWS with MySQL 5.7
           - build_type: centaurDummy
             build_mysql: 5.7
+            friendly_name: Centaur Dummy with MySQL 5.7
           - build_type: centaurHoricromtalPapiV2beta
             build_mysql: 5.7
+            friendly_name: Centaur Horicromtal PapiV2 Beta with MySQL 5.7
           - build_type: horicromtalDeadlock
+            friendly_name: Horicromtal Deadlock
           - build_type: singleWorkflowRunner
-    name: ${{ matrix.build_type }}
+            friendly_name: Single Workflow Runner
+    name: ${{ matrix.friendly_name }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
       BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable

From 4648e5332fbe7351e7fd5c030e72033827c19f87 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 14:40:16 -0500
Subject: [PATCH 209/213] Friendly Names

---
 .github/workflows/integration_tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 0ea68b6050e..80484516e5b 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -19,12 +19,14 @@ jobs:
       fail-fast: false #disabling fail-fast means that even if one test fails, the others will still try to complete.
       #Each entry below is a single integration test that lives in /src/ci/bin/. 
       #Each will be launched on its own runner so they can occur in parallel.
+      #Friendly names are displayed on the Github UI and aren't used anywhere else.
       matrix:
         include:
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
             friendly_name: Centaur Papi V2 Beta with MySQL 5.7
           - build_type: dbms
+            friendly_name: DBMS
           - build_type: centaurTes
             build_mysql: 5.7
             friendly_name: Centaur Tes with MySQL 5.7

From 81246a418f8587e3de27f56fee0e4c3fc6bb51d1 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Feb 2023 15:46:43 -0500
Subject: [PATCH 210/213] Miguel saved a life today

---
 .github/workflows/integration_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 80484516e5b..7964a39cf6e 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -29,7 +29,7 @@ jobs:
             friendly_name: DBMS
           - build_type: centaurTes
             build_mysql: 5.7
-            friendly_name: Centaur Tes with MySQL 5.7
+            friendly_name: Centaur TES with MySQL 5.7
           - build_type: centaurLocal
             build_mysql: 5.7
             friendly_name: Centaur Local with MySQL 5.7
@@ -54,7 +54,7 @@ jobs:
       BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable
       BUILD_MYSQL: ${{ matrix.build_mysql }}
       BUILD_POSTGRESQL: ${{ matrix.build_postgresql }}
-      BUILD_MATRIADB: ${{ matrix.build_mariadb }}
+      BUILD_MARIADB: ${{ matrix.build_mariadb }}
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
     runs-on: ubuntu-latest

From dbfb293bfa8fdb4f009a640501ba0bbc0c0db52f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 16 Feb 2023 15:02:54 -0500
Subject: [PATCH 211/213] testing

---
 .github/workflows/integration_tests.yml | 14 ++++++++++++++
 src/ci/bin/test.inc.sh                  |  3 ++-
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 7964a39cf6e..5a8db86cc64 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -48,6 +48,20 @@ jobs:
             friendly_name: Horicromtal Deadlock
           - build_type: singleWorkflowRunner
             friendly_name: Single Workflow Runner
+          - build_type: centaurLocal
+            build_mariadb: 10.3
+            friendly_name: Centaur Local with MariaDB 10.3
+          - build_type: centaurLocal
+            build_postgresql: 11.3
+            friendly_name: Centaur Local with PostgreSQL 11.3
+          - build_type: centaurEngineUpgradeLocal
+            build_mysql: 5.7
+            friendly_name: Centaur Engine Upgrade Local with MySQL 5.7
+          - build_type: centaurSlurm
+            build_mysql: 5.7
+            friendly_name: Centaur Slurm with MySQL 5.7
+          - build_type: referenceDiskManifestBuilderApp
+            friendly_name: Reference Disk Manifest Builder App
     name: ${{ matrix.friendly_name }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index fe6d8cbbdd8..a5d9d4fe509 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -652,7 +652,8 @@ cromwell::private::create_centaur_variables() {
     # Pick **one** of the databases to run Centaur against
     case "${CROMWELL_BUILD_PROVIDER}" in
         "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
+        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
 
             if [[ -n "${CROMWELL_BUILD_MYSQL_DOCKER_TAG:+set}" ]]; then
                 CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="slick.jdbc.MySQLProfile$"

From e0ff370008fa74d7ca24bcd6b2a6dc8cd05a577c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 16 Feb 2023 16:01:20 -0500
Subject: [PATCH 212/213] back out overzealous tests

---
 .github/workflows/integration_tests.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 5a8db86cc64..8c0397245a7 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -57,11 +57,6 @@ jobs:
           - build_type: centaurEngineUpgradeLocal
             build_mysql: 5.7
             friendly_name: Centaur Engine Upgrade Local with MySQL 5.7
-          - build_type: centaurSlurm
-            build_mysql: 5.7
-            friendly_name: Centaur Slurm with MySQL 5.7
-          - build_type: referenceDiskManifestBuilderApp
-            friendly_name: Reference Disk Manifest Builder App
     name: ${{ matrix.friendly_name }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}

From f227458cadfdf2aa1e70592df8bd3c8640de0be1 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 17 Feb 2023 16:02:37 -0500
Subject: [PATCH 213/213] make tests trigger on merge queue

---
 .github/workflows/cromwell_unit_tests.yml | 1 +
 .github/workflows/integration_tests.yml   | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index d0927f8b954..797f38efd96 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -9,6 +9,7 @@ run-name: ${{ github.actor }} running Cromwell sbt unit tests.
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
   push:
+  merge_group:
 
 permissions: 
   contents: read
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 8c0397245a7..489e9e731a9 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -9,6 +9,7 @@ run-name: ${{ github.actor }} Integration Testing.
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
   push: #git push
+  merge_group:
 
 permissions: 
   contents: read