Merge pull request #139 from broadinstitute/dp-trs-build

dockstore 1.9 integration
broadinstitute · Jul 6, 2020 · d1d12a5 · d1d12a5
2 parents d1790fc + ec7e4df
commit d1d12a5
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Showing 14 changed files with 302 additions and 70 deletions.
diff --git a/.dockerignore b/.dockerignore
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -0,0 +1,227 @@
+version: 1.2
+workflows:
+ - name: align_and_count_multiple_report
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/align_and_count_multiple_report.wdl
+   testParameterFiles:
+    - empty.json
+ - name: align_and_count
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/align_and_count.wdl
+   testParameterFiles:
+    - empty.json
+ - name: align_and_plot
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/align_and_plot.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-align_and_plot-local.json
+ - name: assemble_denovo
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/assemble_denovo.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-assemble_denovo-local.json
+ - name: assemble_refbased
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/assemble_refbased.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-assemble_refbased-local.json
+ - name: augur_from_assemblies
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/augur_from_assemblies.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-augur_from_assemblies-local.json
+ - name: augur_from_beast_mcc
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/augur_from_beast_mcc.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-augur_from_beast_mcc-local.json
+ - name: augur_from_msa
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/augur_from_msa.wdl
+   testParameterFiles:
+    - empty.json
+ - name: augur_from_newick
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/augur_from_newick.wdl
+   testParameterFiles:
+    - empty.json
+ - name: bams_multiqc
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/bams_multiqc.wdl
+   testParameterFiles:
+    - empty.json
+ - name: beast_gpu
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/beast_gpu.wdl
+   testParameterFiles:
+    - empty.json
+ - name: classify_kaiju
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/classify_kaiju.wdl
+   testParameterFiles:
+    - empty.json
+ - name: classify_kraken2
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/classify_kraken2.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-classify_kraken2-local.json
+ - name: classify_krakenuniq
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/classify_krakenuniq.wdl
+   testParameterFiles:
+    - empty.json
+ - name: classify_multi
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/classify_multi.wdl
+   testParameterFiles:
+    - empty.json
+ - name: classify_single
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/classify_single.wdl
+   testParameterFiles:
+    - empty.json
+ - name: contigs
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/contigs.wdl
+   testParameterFiles:
+    - empty.json
+ - name: coverage_table
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/coverage_table.wdl
+   testParameterFiles:
+    - empty.json
+ - name: demux_metag
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/demux_metag.wdl
+   testParameterFiles:
+    - empty.json
+ - name: demux_only
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/demux_only.wdl
+   testParameterFiles:
+    - empty.json
+ - name: demux_plus
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/demux_plus.wdl
+   testParameterFiles:
+    - empty.json
+ - name: deplete_only
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/deplete_only.wdl
+   testParameterFiles:
+    - empty.json
+ - name: diff_genome_sets
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/diff_genome_sets.wdl
+   testParameterFiles:
+    - empty.json
+ - name: downsample
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/downsample.wdl
+   testParameterFiles:
+    - empty.json
+ - name: fastq_to_ubam
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/fastq_to_ubam.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-fastq_to_ubam-local.json
+ - name: fetch_annotations
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/fetch_annotations.wdl
+   testParameterFiles:
+    - empty.json
+ - name: fetch_sra_to_bam
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/fetch_sra_to_bam.wdl
+   testParameterFiles:
+    - empty.json
+ - name: filter_classified_bam_to_taxa
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl
+   testParameterFiles:
+    - empty.json
+ - name: filter_sequences
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/filter_sequences.wdl
+   testParameterFiles:
+    - empty.json
+ - name: genbank
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/genbank.wdl
+   testParameterFiles:
+    - test/input/WDL/test_inputs-genbank-local.json
+ - name: isnvs_merge_to_vcf
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/isnvs_merge_to_vcf.wdl
+   testParameterFiles:
+    - empty.json
+ - name: isnvs_one_sample
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/isnvs_one_sample.wdl
+   testParameterFiles:
+    - empty.json
+ - name: kraken2_build
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/kraken2_build.wdl
+   testParameterFiles:
+    - empty.json
+ - name: mafft_and_snp
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/mafft_and_snp.wdl
+   testParameterFiles:
+    - empty.json
+ - name: mafft_and_trim
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/mafft_and_trim.wdl
+   testParameterFiles:
+    - empty.json
+ - name: mafft
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/mafft.wdl
+   testParameterFiles:
+    - empty.json
+ - name: merge_bams
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/merge_bams.wdl
+   testParameterFiles:
+    - empty.json
+ - name: merge_metagenomics
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/merge_metagenomics.wdl
+   testParameterFiles:
+    - empty.json
+ - name: merge_tar_chunks
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/merge_tar_chunks.wdl
+   testParameterFiles:
+    - empty.json
+ - name: merge_vcfs_and_annotate
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/merge_vcfs_and_annotate.wdl
+   testParameterFiles:
+    - empty.json
+ - name: merge_vcfs
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/merge_vcfs.wdl
+   testParameterFiles:
+    - empty.json
+ - name: multiqc_only
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/multiqc_only.wdl
+   testParameterFiles:
+    - empty.json
+ - name: scaffold_and_refine
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/scaffold_and_refine.wdl
+   testParameterFiles:
+    - empty.json
+ - name: subsample_by_metadata
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/subsample_by_metadata.wdl
+   testParameterFiles:
+    - empty.json
+ - name: trimal
+   subclass: WDL
+   primaryDescriptorPath: pipes/WDL/workflows/trimal.wdl
+   testParameterFiles:
+    - empty.json
diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl
@@ -16,7 +16,7 @@ task assemble {
       String   sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt")
 
       Int?     machine_mem_gb
-      String   docker="quay.io/broadinstitute/viral-assemble"
+      String   docker="quay.io/broadinstitute/viral-assemble:2.1.4.0"
     }
 
     command {
@@ -114,7 +114,7 @@ task scaffold {
       Float?       scaffold_min_pct_contig_aligned
 
       Int?         machine_mem_gb
-      String       docker="quay.io/broadinstitute/viral-assemble"
+      String       docker="quay.io/broadinstitute/viral-assemble:2.1.4.0"
 
       # do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
       String       sample_name = basename(basename(basename(contigs_fasta, ".fasta"), ".assembly1-trinity"), ".assembly1-spades")
@@ -201,7 +201,7 @@ task ivar_trim {
       Int?    min_quality=1
 
       Int?    machine_mem_gb
-      String  docker="andersenlabapps/ivar"
+      String  docker="andersenlabapps/ivar:1.2.2"
     }
 
     String  bam_basename=basename(aligned_bam, ".bam")
@@ -259,7 +259,7 @@ task align_reads {
     String?  aligner_options
     Boolean? skip_mark_dupes=false
 
-    String   docker="quay.io/broadinstitute/viral-core"
+    String   docker="quay.io/broadinstitute/viral-core:2.1.8"
 
     String   sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
   }
@@ -373,7 +373,7 @@ task refine_assembly_with_aligned_reads {
       Int?     min_coverage=3
 
       Int?     machine_mem_gb
-      String   docker="quay.io/broadinstitute/viral-assemble"
+      String   docker="quay.io/broadinstitute/viral-assemble:2.1.4.0"
     }
 
     parameter_meta {
@@ -465,7 +465,7 @@ task refine {
       Int?    min_coverage=1
 
       Int?    machine_mem_gb
-      String  docker="quay.io/broadinstitute/viral-assemble"
+      String  docker="quay.io/broadinstitute/viral-assemble:2.1.4.0"
 
       String  assembly_basename=basename(basename(assembly_fasta, ".fasta"), ".scaffold")
     }
@@ -535,7 +535,7 @@ task refine_2x_and_plot {
       String? plot_coverage_novoalign_options="-r Random -l 40 -g 40 -x 20 -t 100 -k"
 
       Int?    machine_mem_gb
-      String  docker="quay.io/broadinstitute/viral-assemble"
+      String  docker="quay.io/broadinstitute/viral-assemble:2.1.4.0"
 
       # do this in two steps in case the input doesn't actually have "cleaned" in the name
       String  sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
@@ -667,7 +667,7 @@ task run_discordance {
       String   out_basename = "run"
       Int      min_coverage=4
 
-      String   docker="quay.io/broadinstitute/viral-core"
+      String   docker="quay.io/broadinstitute/viral-core:2.1.8"
     }
 
     command {

diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl
@@ -6,7 +6,7 @@ task merge_tarballs {
     String        out_filename
 
     Int?          machine_mem_gb
-    String        docker="quay.io/broadinstitute/viral-core"
+    String        docker="quay.io/broadinstitute/viral-core:2.1.8"
   }
 
   command {
@@ -60,7 +60,7 @@ task illumina_demux {
     Boolean? forceGC=true
 
     Int?    machine_mem_gb
-    String  docker="quay.io/broadinstitute/viral-core"
+    String  docker="quay.io/broadinstitute/viral-core:2.1.8"
   }
 
   command {

diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl
@@ -9,7 +9,7 @@ task multi_align_mafft_ref {
     Float?         mafft_gapOpeningPenalty
 
     Int?           machine_mem_gb
-    String         docker="quay.io/broadinstitute/viral-phylo"
+    String         docker="quay.io/broadinstitute/viral-phylo:2.1.4.0"
   }
 
   String           fasta_basename = basename(reference_fasta, '.fasta')
@@ -53,7 +53,7 @@ task multi_align_mafft {
     Float?         mafft_gapOpeningPenalty
 
     Int?           machine_mem_gb
-    String         docker="quay.io/broadinstitute/viral-phylo"
+    String         docker="quay.io/broadinstitute/viral-phylo:2.1.4.0"
   }
 
   command {
@@ -90,7 +90,7 @@ task beast {
   input {
     File     beauti_xml
 
-    String   docker="quay.io/broadinstitute/beast-beagle-cuda"
+    String   docker="quay.io/broadinstitute/beast-beagle-cuda:1.10.5pre"
   }
 
   # TO DO: parameterize gpuType and gpuCount
@@ -137,7 +137,7 @@ task index_ref {
     File?    novocraft_license
 
     Int?     machine_mem_gb
-    String   docker="quay.io/broadinstitute/viral-core"
+    String   docker="quay.io/broadinstitute/viral-core:2.1.8"
   }
 
   command {
@@ -247,7 +247,7 @@ task merge_vcfs_gatk {
     File        ref_fasta
 
     Int?     machine_mem_gb
-    String   docker="quay.io/broadinstitute/viral-phylo"
+    String   docker="quay.io/broadinstitute/viral-phylo:2.1.4.0"
 
     String   output_prefix = "merged"
   }

diff --git a/pipes/WDL/tasks/tasks_intrahost.wdl b/pipes/WDL/tasks/tasks_intrahost.wdl
@@ -10,7 +10,7 @@ task isnvs_per_sample {
     Int?    maxBias
 
     Int?    machine_mem_gb
-    String  docker="quay.io/broadinstitute/viral-phylo"
+    String  docker="quay.io/broadinstitute/viral-phylo:2.1.4.0"
 
     String  sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
   }
@@ -51,7 +51,7 @@ task isnvs_vcf {
     Boolean        naiveFilter=false
 
     Int?           machine_mem_gb
-    String         docker="quay.io/broadinstitute/viral-phylo"
+    String         docker="quay.io/broadinstitute/viral-phylo:2.1.4.0"
   }
 
   parameter_meta {
@@ -124,7 +124,7 @@ task annotate_vcf_snpeff {
     String?        emailAddress
 
     Int?           machine_mem_gb
-    String         docker="quay.io/broadinstitute/viral-phylo"
+    String         docker="quay.io/broadinstitute/viral-phylo:2.1.4.0"
 
     String         output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
   }