output viral-ngs version as string in WDL workflows

This calls `reports.py --version` in a new WDL task at the end of each workflow.
broadinstitute · Feb 15, 2019 · 40c020f · 40c020f
1 parent bb85497
commit 40c020f
Show file tree

Hide file tree

Showing 24 changed files with 77 additions and 1 deletion.
diff --git a/pipes/WDL/workflows/align_and_plot.wdl b/pipes/WDL/workflows/align_and_plot.wdl
@@ -5,4 +5,6 @@ workflow align_and_plot {
         input:
             aligner_options = "-r Random -l 30 -g 40 -x 20 -t 502"
     }
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/assemble_denovo.wdl b/pipes/WDL/workflows/assemble_denovo.wdl
@@ -1,5 +1,6 @@
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
+import "tasks_reports.wdl" as reports
 
 workflow assemble_denovo {
 
@@ -26,4 +27,6 @@ workflow assemble_denovo {
       assembly_fasta = scaffold.scaffold_fasta,
       reads_unmapped_bam = reads_unmapped_bam
   }
+
+  call reports.software_version
 }
diff --git a/pipes/WDL/workflows/assemble_denovo_with_deplete.wdl b/pipes/WDL/workflows/assemble_denovo_with_deplete.wdl
@@ -1,5 +1,6 @@
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
+import "tasks_reports.wdl" as reports
 
 workflow assemble_denovo_with_deplete {
 
@@ -26,4 +27,6 @@ workflow assemble_denovo_with_deplete {
       assembly_fasta = scaffold.scaffold_fasta,
       reads_unmapped_bam = deplete_taxa.cleaned_bam
   }
+
+  call reports.software_version
 }
diff --git a/pipes/WDL/workflows/assemble_denovo_with_deplete_and_isnv_calling.wdl b/pipes/WDL/workflows/assemble_denovo_with_deplete_and_isnv_calling.wdl
@@ -1,6 +1,7 @@
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
 import "tasks_intrahost.wdl" as intrahost
+import "tasks_reports.wdl" as reports
 
 workflow assemble_denovo_with_deplete_and_isnv_calling {
 
@@ -33,4 +34,6 @@ workflow assemble_denovo_with_deplete_and_isnv_calling {
       assembly_fasta = refine_2x_and_plot.final_assembly_fasta,
       mapped_bam = refine_2x_and_plot.aligned_bam
   }
+
+  call reports.software_version
 }
diff --git a/pipes/WDL/workflows/assemble_denovo_with_isnv_calling.wdl b/pipes/WDL/workflows/assemble_denovo_with_isnv_calling.wdl
@@ -1,6 +1,7 @@
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
 import "tasks_intrahost.wdl" as intrahost
+import "tasks_reports.wdl" as reports
 
 workflow assemble_denovo_with_isnv_calling {
     File reads_unmapped_bam
@@ -32,4 +33,6 @@ workflow assemble_denovo_with_isnv_calling {
             assembly_fasta = refine_2x_and_plot.final_assembly_fasta,
             mapped_bam = refine_2x_and_plot.aligned_bam
     }
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/assemble_refbased.wdl b/pipes/WDL/workflows/assemble_refbased.wdl
@@ -1,5 +1,7 @@
 import "tasks_assembly.wdl" as assembly
+import "tasks_reports.wdl" as reports
 
 workflow assemble_refbased {
   call assembly.refine_2x_and_plot
+  call reports.software_version
 }
diff --git a/pipes/WDL/workflows/classify_kraken.wdl b/pipes/WDL/workflows/classify_kraken.wdl
@@ -1,5 +1,7 @@
 import "tasks_metagenomics.wdl" as metagenomics
+import "tasks_reports.wdl" as reports
 
 workflow classify_kraken {
     call metagenomics.kraken
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/contigs.wdl b/pipes/WDL/workflows/contigs.wdl
@@ -1,6 +1,7 @@
 import "tasks_metagenomics.wdl" as metagenomics
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
+import "tasks_reports.wdl" as reports
 
 workflow contigs {
 
@@ -14,4 +15,6 @@ workflow contigs {
 
   # TO DO: taxonomic classification of contigs
 
+    call reports.software_version
+
 }
diff --git a/pipes/WDL/workflows/coverage_table.wdl b/pipes/WDL/workflows/coverage_table.wdl
@@ -1,5 +1,7 @@
 import "tasks_reports.wdl" as reports
+import "tasks_reports.wdl" as reports
 
 workflow coverage_table {
     call reports.coverage_report
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/demux_metag.wdl b/pipes/WDL/workflows/demux_metag.wdl
@@ -5,6 +5,7 @@ import "tasks_metagenomics.wdl" as metagenomics
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
 import "tasks_reports.wdl" as reports
+import "tasks_reports.wdl" as reports
 
 workflow demux_metag {
   File krona_taxonomy_db_tgz
@@ -39,4 +40,6 @@ workflow demux_metag {
       krona_taxonomy_db_tgz = krona_taxonomy_db_tgz
   }
 
+  call reports.software_version
+
 }
diff --git a/pipes/WDL/workflows/demux_only.wdl b/pipes/WDL/workflows/demux_only.wdl
@@ -1,5 +1,7 @@
 import "tasks_demux.wdl" as tasks_demux
+import "tasks_reports.wdl" as reports
 
 workflow demux_only {
     call tasks_demux.illumina_demux
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/demux_plus.wdl b/pipes/WDL/workflows/demux_plus.wdl
@@ -3,6 +3,7 @@ import "tasks_metagenomics.wdl" as metagenomics
 import "tasks_taxon_filter.wdl" as taxon_filter
 import "tasks_assembly.wdl" as assembly
 import "tasks_reports.wdl" as reports
+import "tasks_reports.wdl" as reports
 
 workflow demux_plus {
 
@@ -39,4 +40,6 @@ workflow demux_plus {
         input:
             reads_unmapped_bam = illumina_demux.raw_reads_unaligned_bams
     }
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/deplete_only.wdl b/pipes/WDL/workflows/deplete_only.wdl
@@ -1,5 +1,7 @@
 import "tasks_taxon_filter.wdl" as taxon_filter
+import "tasks_reports.wdl" as reports
 
 workflow deplete_only {
-    call taxon_filter.deplete_taxa 
+    call taxon_filter.deplete_taxa
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/fetch_annotations.wdl b/pipes/WDL/workflows/fetch_annotations.wdl
@@ -1,5 +1,7 @@
 import "tasks_ncbi.wdl" as ncbi
+import "tasks_reports.wdl" as reports
 
 workflow fetch_annotations {
     call ncbi.download_annotations
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl b/pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl
@@ -1,5 +1,7 @@
 import "tasks_metagenomics.wdl" as metagenomics
+import "tasks_reports.wdl" as reports
 
 workflow filter_classified_bam_to_taxa {
     call metagenomics.filter_bam_to_taxa
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/genbank.wdl b/pipes/WDL/workflows/genbank.wdl
@@ -1,5 +1,6 @@
 import "tasks_interhost.wdl" as interhost
 import "tasks_ncbi.wdl" as ncbi
+import "tasks_reports.wdl" as reports
 
 workflow genbank {
 
@@ -23,4 +24,6 @@ workflow genbank {
             assemblies_fasta = assemblies_fasta,
             annotations_tbl = annot.transferred_feature_tables
     }
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/isnvs_merge_to_vcf.wdl b/pipes/WDL/workflows/isnvs_merge_to_vcf.wdl
@@ -1,5 +1,6 @@
 import "tasks_interhost.wdl" as interhost
 import "tasks_intrahost.wdl" as tasks_intrahost
+import "tasks_reports.wdl" as reports
 
 workflow isnvs_merge_to_vcf {
     File          reference_fasta
@@ -10,9 +11,12 @@ workflow isnvs_merge_to_vcf {
             reference_fasta = reference_fasta,
             assemblies_fasta = assemblies_fasta
     }
+
     call tasks_intrahost.isnvs_vcf {
         input:
             perSegmentMultiAlignments = mafft.alignments_by_chr,
             reference_fasta = reference_fasta
     }
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/isnvs_one_sample.wdl b/pipes/WDL/workflows/isnvs_one_sample.wdl
@@ -1,5 +1,7 @@
 import "tasks_intrahost.wdl" as intrahost
+import "tasks_reports.wdl" as reports
 
 workflow isnvs_one_sample {
     call intrahost.isnvs_per_sample
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/mafft.wdl b/pipes/WDL/workflows/mafft.wdl
@@ -1,5 +1,7 @@
 import "tasks_interhost.wdl" as interhost
+import "tasks_reports.wdl" as reports
 
 workflow mafft {
     call interhost.multi_align_mafft
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/merge_bams.wdl b/pipes/WDL/workflows/merge_bams.wdl
@@ -1,5 +1,7 @@
 import "tasks_demux.wdl" as demux
+import "tasks_reports.wdl" as reports
 
 workflow merge_bams {
     call demux.merge_and_reheader_bams
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/read_utils.wdl b/pipes/WDL/workflows/read_utils.wdl
@@ -1,5 +1,7 @@
 import "tasks_read_utils.wdl" as reads
+import "tasks_reports.wdl" as reports
 
 workflow downsample {
     call reads.downsample_bams
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/scaffold_and_refine.wdl b/pipes/WDL/workflows/scaffold_and_refine.wdl
@@ -1,4 +1,5 @@
 import "tasks_assembly.wdl" as assembly
+import "tasks_reports.wdl" as reports
 
 workflow scaffold_and_refine {
     File reads_unmapped_bam
@@ -13,4 +14,6 @@ workflow scaffold_and_refine {
             assembly_fasta = scaffold.scaffold_fasta,
             reads_unmapped_bam = reads_unmapped_bam
     }
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/spikein.wdl b/pipes/WDL/workflows/spikein.wdl
@@ -1,5 +1,8 @@
 import "tasks_reports.wdl" as reports
+import "tasks_reports.wdl" as reports
 
 workflow spikein {
     call reports.spikein_report
+
+    call reports.software_version
 }
diff --git a/pipes/WDL/workflows/tasks/tasks_reports.wdl b/pipes/WDL/workflows/tasks/tasks_reports.wdl
@@ -186,4 +186,22 @@ task spikein_report {
   }
 }
 
+task software_version {
+  command {
+    set -ex -o pipefail
+    reports.py --version > "current_software_version.txt"
+  }
+
+  output {
+    String software_version = read_string("current_software_version.txt")
+  }
+
+  runtime {
+    memory: "2 GB"
+    cpu: 1
+    docker: "quay.io/broadinstitute/viral-ngs"
+    dx_instance_type: "mem1_ssd1_x4"
+  }
+}
+