Merge branch 'master' into ct-demux_deplete-allow_multiple_biosample_…

…attribute_files

.github/workflows/build.yml

@@ -10,6 +10,12 @@ on:
     types:
       - created
 
+concurrency:
+  # Group jobs by the branch or tag ref to ensure only one job runs for a ref at a time
+  group: ${{ github.ref }}
+  # Cancel any in-progress jobs for the same group
+  cancel-in-progress: true
+
 env:
   PYTHONIOENCODING: UTF8
   DOCKER_REGISTRY: "quay.io"
@@ -32,6 +38,8 @@ env:
 
 jobs:
   validate_wdl_miniwdl:
+    # Run if not a push event or if there's no pull request for the branch
+    if: github.event_name != 'push' || github.event.pull_request == null
     runs-on: ubuntu-20.04
     steps:
       - name: checkout repository
@@ -85,6 +93,8 @@ jobs:
           miniwdl check pipes/WDL/workflows/*.wdl
 
   validate_wdl_womtool:
+    # Run if not a push event or if there's no pull request for the branch
+    if: github.event_name != 'push' || github.event.pull_request == null
     runs-on: ubuntu-20.04
     steps:
       - name: checkout repository
@@ -135,6 +145,8 @@ jobs:
   ## readthedocs does its own build trigger. this job exists simply to 
   ## attempt a build and alert us of documentation build failures because otherwise we would never know.
   test_docs:
+    # Run if not a push event or if there's no pull request for the branch
+    if: github.event_name != 'push' || github.event.pull_request == null
     runs-on: ubuntu-20.04
     steps:
       - name: checkout repository
@@ -179,6 +191,8 @@ jobs:
           github_actions_ci/build-docs.sh
 
   test_cromwell:
+    # Run if not a push event or if there's no pull request for the branch
+    if: github.event_name != 'push' || github.event.pull_request == null
     needs: validate_wdl_womtool
     runs-on: ubuntu-20.04
     steps:
@@ -234,6 +248,8 @@ jobs:
           github_actions_ci/tests-cromwell.sh
 
   test_miniwdl:
+    # Run if not a push event or if there's no pull request for the branch
+    if: github.event_name != 'push' || github.event.pull_request == null
     needs: validate_wdl_miniwdl
     runs-on: ubuntu-20.04
     steps:

pipes/WDL/workflows/augur_from_assemblies.wdl

@@ -67,9 +67,13 @@ workflow augur_from_assemblies {
             sequences_fasta = zcat.combined,
             min_non_N       = min_unambig_genome
     }
+    call nextstrain.nextstrain_deduplicate_sequences as dedup_seqs {
+        input:
+            sequences_fasta = filter_sequences_by_length.filtered_fasta
+    }
     call nextstrain.mafft_one_chr as mafft {
         input:
-            sequences = filter_sequences_by_length.filtered_fasta,
+            sequences = dedup_seqs.sequences_deduplicated_fasta,
             ref_fasta = ref_fasta,
             basename  = "all_samples_aligned.fasta"
     }