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 001/137] 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 002/137] 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 003/137] 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 004/137] 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 005/137] 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 006/137] 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 007/137] 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 008/137] 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 009/137] 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 010/137] 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 011/137] 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 012/137] 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 013/137] 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 014/137] 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 015/137] 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 016/137] 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 017/137] 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 018/137] 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 019/137] 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 020/137] 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 021/137] 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 022/137] 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 023/137] 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 024/137] 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 025/137] 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 026/137] 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 027/137] 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 028/137] 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 029/137] 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 030/137] 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 031/137] 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 032/137] 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 033/137] 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 034/137] 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 035/137] 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 036/137] 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 037/137] 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 038/137] 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 039/137] 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 040/137] 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 041/137] 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 042/137] 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 043/137] 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 044/137] 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 045/137] 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 046/137] 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 047/137] 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 048/137] 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 049/137] 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 050/137] 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 051/137] 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 052/137] 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 053/137] 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 054/137] 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 055/137] 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 056/137] 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 057/137] 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 058/137] 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 059/137] 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 060/137] 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 061/137] 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 062/137] 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 063/137] 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 064/137] 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 065/137] 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 066/137] 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 067/137] 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 068/137] 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 069/137] 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 070/137] 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 071/137] 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 072/137] 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 073/137] \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 074/137] 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 075/137] 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 076/137] 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 077/137] 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 078/137] 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 079/137] 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 080/137] 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 081/137] 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 082/137] 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 083/137] 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 084/137] 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 085/137] 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 086/137] 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 087/137] 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 088/137] 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 089/137] 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 090/137] 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 091/137] 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 092/137] 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 093/137] 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 094/137] 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 095/137] 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 096/137] 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 097/137] 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 098/137] 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 099/137] 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 100/137] 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 101/137] 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 102/137] 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 103/137] 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 104/137] 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 105/137] 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 106/137] 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 107/137] 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 108/137] 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 109/137] 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 110/137] 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 111/137] 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 112/137] 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 113/137] 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 114/137] 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 115/137] 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 116/137] 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 117/137] 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 118/137] 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 119/137] 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 120/137] 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 121/137] 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 122/137] 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 123/137] 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 124/137] 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 125/137] 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 126/137] 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 127/137] 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 128/137] 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 129/137] 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 130/137] 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 131/137] 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 132/137] 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 133/137] 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 134/137] 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 135/137] 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 136/137] 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 137/137] 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