Merge pull request #595 from broadinstitute/dp-build-fix

Fix GH Actions builds

Author: dpark01

.github/workflows/build.yml

@@ -42,7 +42,7 @@ 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
+    runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
@@ -97,7 +97,7 @@ jobs:
   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
+    runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
@@ -149,7 +149,7 @@ jobs:
   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
+    runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
@@ -196,7 +196,7 @@ jobs:
     # 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
+    runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
@@ -253,7 +253,7 @@ jobs:
     # 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
+    runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
@@ -318,7 +318,7 @@ jobs:
     needs:
       - validate_wdl_womtool
       - validate_wdl_miniwdl
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
       # DX_API_TOKEN (for DNAnexus builds) -- GitHub Actions token #1, expires 2025-01-17
       # stored here: https://github.com/broadinstitute/viral-pipelines/settings/secrets/actions

pipes/WDL/workflows/assemble_denovo.wdl

@@ -195,7 +195,7 @@ workflow assemble_denovo {
     File    aligned_only_reads_fastqc             = refine.align_to_ref_fastqc
     File    coverage_tsv                          = refine.align_to_self_merged_coverage_tsv
     Int     read_pairs_aligned                    = refine.align_to_self_merged_read_pairs_aligned
-    Float   bases_aligned                         = refine.align_to_self_merged_bases_aligned
+    Int     bases_aligned                         = refine.align_to_self_merged_bases_aligned
 
     String  assembly_method = "viral-ngs/assemble_denovo"
     String  assemble_viral_assemble_version       = assemble.viralngs_version

pipes/WDL/workflows/assemble_refbased.wdl

@@ -222,7 +222,7 @@ workflow assemble_refbased {
         File        align_to_ref_merged_coverage_tsv             = plot_ref_coverage.coverage_tsv
         Int         align_to_ref_merged_reads_aligned            = plot_ref_coverage.reads_aligned
         Int         align_to_ref_merged_read_pairs_aligned       = plot_ref_coverage.read_pairs_aligned
-        Float       align_to_ref_merged_bases_aligned            = plot_ref_coverage.bases_aligned
+        Int         align_to_ref_merged_bases_aligned            = floor(plot_ref_coverage.bases_aligned)
         File        align_to_ref_isnvs_vcf                       = isnvs_ref.report_vcf
 
         File        picard_metrics_wgs                           = alignment_metrics.wgs_metrics
@@ -238,7 +238,7 @@ workflow assemble_refbased {
         File        align_to_self_merged_coverage_tsv            = plot_self_coverage.coverage_tsv
         Int         align_to_self_merged_reads_aligned           = plot_self_coverage.reads_aligned
         Int         align_to_self_merged_read_pairs_aligned      = plot_self_coverage.read_pairs_aligned
-        Float       align_to_self_merged_bases_aligned           = plot_self_coverage.bases_aligned
+        Int         align_to_self_merged_bases_aligned           = floor(plot_self_coverage.bases_aligned)
         Float       align_to_self_merged_mean_coverage           = plot_self_coverage.mean_coverage
         File        align_to_self_isnvs_vcf                      = isnvs_self.report_vcf