From 0ab1c2a37017b339d500c5b1cf55735b19cca5d9 Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Thu, 18 Jul 2019 12:50:38 -0500 Subject: [PATCH 1/6] New type to represent sequence data. --- definitions/tools/sequence_align_and_tag.cwl | 83 ++++++++++++++++++++ definitions/types/sequence_data.yml | 20 +++++ 2 files changed, 103 insertions(+) create mode 100644 definitions/tools/sequence_align_and_tag.cwl create mode 100644 definitions/types/sequence_data.yml diff --git a/definitions/tools/sequence_align_and_tag.cwl b/definitions/tools/sequence_align_and_tag.cwl new file mode 100644 index 000000000..02a2b87a3 --- /dev/null +++ b/definitions/tools/sequence_align_and_tag.cwl @@ -0,0 +1,83 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: CommandLineTool +label: "align with bwa_mem and tag" + +baseCommand: ["/bin/bash", "sequence_alignment_helper.sh"] +requirements: + - class: SchemaDefRequirement + types: + - $import: ../types/sequence_data.yml + - class: ResourceRequirement + coresMin: 8 + ramMin: 20000 + # - class: DockerRequirement + # dockerPull: "mgibio/alignment_helper-cwl:1.0.0" + - class: InlineJavascriptRequirement #necessary for cwltool to handle the record + - class: InitialWorkDirRequirement + listing: + - entryname: 'sequence_alignment_helper.sh' + entry: | + set -o pipefail + set -o errexit + set -o nounset + + while getopts "b:?1:?2:?g:r:n:" opt; do + case "$opt" in + b) + MODE=bam + BAM="$OPTARG" + ;; + 1) + MODE=fastq + FASTQ1="$OPTARG" + ;; + 2) + MODE=fastq + FASTQ2="$OPTARG" + ;; + g) + READGROUP="$OPTARG" + ;; + r) + REFERENCE="$OPTARG" + ;; + n) + NTHREADS="$OPTARG" + ;; + esac + done + + if [[ "$MODE" == 'fastq' ]]; then + echo /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" "$FASTQ1" "$FASTQ2" "|" /usr/local/bin/samblaster -a --addMateTags "|" /opt/samtools/bin/samtools view -b -S /dev/stdin + fi + if [[ "$MODE" == 'bam' ]]; then + echo /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I="$BAM" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout "|" /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" /dev/stdin "|" /usr/local/bin/samblaster -a --addMateTags "|" /opt/samtools/bin/samtools view -b -S /dev/stdin + fi +stdout: "refAlign.bam" +arguments: + - valueFrom: $(runtime.cores) + position: 5 + prefix: '-n' + - valueFrom: $(inputs.unaligned.sequence.bam) + prefix: '-b' + - valueFrom: $(inputs.unaligned.sequence.fastq1) + prefix: '-1' + - valueFrom: $(inputs.unaligned.sequence.fastq2) + prefix: '-2' + - valueFrom: $(inputs.unaligned.readgroup) + prefix: '-g' +inputs: + unaligned: + type: ../types/sequence_data.yml#sequence_data + doc: "the unaligned sequence data with readgroup information" + reference: + type: string + inputBinding: + position: 4 + prefix: '-r' + doc: 'bwa-indexed reference file' +outputs: + aligned_bam: + type: stdout diff --git a/definitions/types/sequence_data.yml b/definitions/types/sequence_data.yml new file mode 100644 index 000000000..324e059a2 --- /dev/null +++ b/definitions/types/sequence_data.yml @@ -0,0 +1,20 @@ +type: record +name: sequence_data +label: sequence data with readgroup information +fields: + sequence: + type: + - type: record + name: bam + fields: + bam: + type: File + - type: record + name: fastqs + fields: + fastq1: + type: File + fastq2: + type: File + readgroup: + type: string From 69ecfe2188e24832bdd1e9033b7b6b0a79618cb9 Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Thu, 18 Jul 2019 12:50:48 -0500 Subject: [PATCH 2/6] New tool to align sequence data regardless of filetype. --- definitions/tools/sequence_align_and_tag.cwl | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/definitions/tools/sequence_align_and_tag.cwl b/definitions/tools/sequence_align_and_tag.cwl index 02a2b87a3..151a12aa0 100644 --- a/definitions/tools/sequence_align_and_tag.cwl +++ b/definitions/tools/sequence_align_and_tag.cwl @@ -12,9 +12,9 @@ requirements: - class: ResourceRequirement coresMin: 8 ramMin: 20000 - # - class: DockerRequirement - # dockerPull: "mgibio/alignment_helper-cwl:1.0.0" - - class: InlineJavascriptRequirement #necessary for cwltool to handle the record + - class: DockerRequirement + dockerPull: "mgibio/alignment_helper-cwl:1.0.0" + - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement listing: - entryname: 'sequence_alignment_helper.sh' @@ -50,21 +50,21 @@ requirements: done if [[ "$MODE" == 'fastq' ]]; then - echo /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" "$FASTQ1" "$FASTQ2" "|" /usr/local/bin/samblaster -a --addMateTags "|" /opt/samtools/bin/samtools view -b -S /dev/stdin + /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" "$FASTQ1" "$FASTQ2" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin fi if [[ "$MODE" == 'bam' ]]; then - echo /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I="$BAM" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout "|" /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" /dev/stdin "|" /usr/local/bin/samblaster -a --addMateTags "|" /opt/samtools/bin/samtools view -b -S /dev/stdin + /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I="$BAM" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t "$NTHREADS" -Y -p -R "$READGROUP" "$REFERENCE" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin fi stdout: "refAlign.bam" arguments: - valueFrom: $(runtime.cores) position: 5 prefix: '-n' - - valueFrom: $(inputs.unaligned.sequence.bam) + - valueFrom: "$(inputs.unaligned.sequence.hasOwnProperty('bam')? inputs.unaligned.sequence.bam : null)" prefix: '-b' - - valueFrom: $(inputs.unaligned.sequence.fastq1) + - valueFrom: "$(inputs.unaligned.sequence.hasOwnProperty('fastq1')? inputs.unaligned.sequence.fastq1 : null)" prefix: '-1' - - valueFrom: $(inputs.unaligned.sequence.fastq2) + - valueFrom: "$(inputs.unaligned.sequence.hasOwnProperty('fastq2')? inputs.unaligned.sequence.fastq2 : null)" prefix: '-2' - valueFrom: $(inputs.unaligned.readgroup) prefix: '-g' From eece0dc9601fc5e859ca1d8c002f31ac1330a70b Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Thu, 18 Jul 2019 12:54:58 -0500 Subject: [PATCH 3/6] Subworkflow to perform alignment on "sequence_data". --- definitions/subworkflows/sequence_to_bqsr.cwl | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 definitions/subworkflows/sequence_to_bqsr.cwl diff --git a/definitions/subworkflows/sequence_to_bqsr.cwl b/definitions/subworkflows/sequence_to_bqsr.cwl new file mode 100644 index 000000000..d8af8dfda --- /dev/null +++ b/definitions/subworkflows/sequence_to_bqsr.cwl @@ -0,0 +1,93 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: Workflow +label: "Raw sequence data to BQSR" +requirements: + - class: SchemaDefRequirement + types: + - $import: ../types/sequence_data.yml + - class: ScatterFeatureRequirement + - class: SubworkflowFeatureRequirement + - class: MultipleInputFeatureRequirement + +inputs: + unaligned: + type: ../types/sequence_data.yml#sequence_data[] + bqsr_intervals: + type: string[] + reference: + type: string + dbsnp_vcf: + type: File + secondaryFiles: [.tbi] + final_name: + type: string? + default: 'final.bam' + mills: + type: File + secondaryFiles: [.tbi] + known_indels: + type: File + secondaryFiles: [.tbi] +outputs: + final_bam: + type: File + outputSource: index_bam/indexed_bam + secondaryFiles: [.bai, ^.bai] + mark_duplicates_metrics_file: + type: File + outputSource: mark_duplicates_and_sort/metrics_file +steps: + align: + scatter: [unaligned] + scatterMethod: dotproduct + run: ../tools/sequence_align_and_tag.cwl + in: + unaligned: unaligned + reference: reference + out: + [aligned_bam] + merge: + run: ../tools/merge_bams_samtools.cwl + in: + bams: align/aligned_bam + name: final_name + out: + [merged_bam] + name_sort: + run: ../tools/name_sort.cwl + in: + bam: merge/merged_bam + out: + [name_sorted_bam] + mark_duplicates_and_sort: + run: ../tools/mark_duplicates_and_sort.cwl + in: + bam: name_sort/name_sorted_bam + out: + [sorted_bam, metrics_file] + bqsr: + run: ../tools/bqsr.cwl + in: + reference: reference + bam: mark_duplicates_and_sort/sorted_bam + intervals: bqsr_intervals + known_sites: [dbsnp_vcf, mills, known_indels] + out: + [bqsr_table] + apply_bqsr: + run: ../tools/apply_bqsr.cwl + in: + reference: reference + bam: mark_duplicates_and_sort/sorted_bam + bqsr_table: bqsr/bqsr_table + output_name: final_name + out: + [bqsr_bam] + index_bam: + run: ../tools/index_bam.cwl + in: + bam: apply_bqsr/bqsr_bam + out: + [indexed_bam] From 6259aa50fdbbfaa6bbac51c1728a4f9c9374c5bd Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Mon, 22 Jul 2019 17:00:49 -0500 Subject: [PATCH 4/6] Use new sequence type for standard DNA alignment process. --- definitions/pipelines/cle_aml_trio.cwl | 28 +++++--------- definitions/pipelines/cle_somatic_exome.cwl | 19 ++++------ definitions/pipelines/exome.cwl | 10 ++--- definitions/pipelines/exome_alignment.cwl | 12 +++--- .../pipelines/gathered_cle_aml_trio.cwl | 28 +++++--------- .../pipelines/gathered_cle_somatic_exome.cwl | 19 ++++------ .../pipelines/gathered_somatic_exome.cwl | 19 ++++------ definitions/pipelines/germline_exome.cwl | 10 ++--- .../pipelines/germline_exome_hla_typing.cwl | 10 ++--- definitions/pipelines/germline_wgs.cwl | 10 ++--- definitions/pipelines/immuno.cwl | 22 ++++------- definitions/pipelines/somatic_exome.cwl | 19 ++++------ definitions/pipelines/wgs.cwl | 10 ++--- definitions/pipelines/wgs_alignment.cwl | 12 +++--- .../cle_IDT_somatic_exome_template.yaml | 22 ++++++----- example_data/cle_aml_trio_template.yaml | 33 ++++++++-------- example_data/exome_workflow.yaml | 19 ++++++---- example_data/germline_exome.yaml | 19 ++++++---- example_data/germline_wgs.yaml | 19 ++++++---- example_data/somatic_exome.yaml | 38 +++++++++++-------- 20 files changed, 171 insertions(+), 207 deletions(-) diff --git a/definitions/pipelines/cle_aml_trio.cwl b/definitions/pipelines/cle_aml_trio.cwl index dce91e30a..688c7fa68 100644 --- a/definitions/pipelines/cle_aml_trio.cwl +++ b/definitions/pipelines/cle_aml_trio.cwl @@ -7,28 +7,23 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' - followup_bams: - type: File[] - followup_readgroups: - type: string[] + followup_sequence: + type: ../types/sequence_data.yml#sequence_data[] followup_name: type: string? default: 'followup' @@ -367,8 +362,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: normal_bams - readgroups: normal_readgroups + sequence: normal_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf @@ -391,8 +385,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: tumor_bams - readgroups: tumor_readgroups + sequence: tumor_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf @@ -415,8 +408,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: followup_bams - readgroups: followup_readgroups + sequence: followup_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/cle_somatic_exome.cwl b/definitions/pipelines/cle_somatic_exome.cwl index 3337e329a..413ae0dc9 100644 --- a/definitions/pipelines/cle_somatic_exome.cwl +++ b/definitions/pipelines/cle_somatic_exome.cwl @@ -7,21 +7,18 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' @@ -295,8 +292,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: tumor_bams - readgroups: tumor_readgroups + sequence: tumor_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf @@ -319,8 +315,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: normal_bams - readgroups: normal_readgroups + sequence: normal_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/exome.cwl b/definitions/pipelines/exome.cwl index 8048641b7..148b6c7fa 100644 --- a/definitions/pipelines/exome.cwl +++ b/definitions/pipelines/exome.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -179,8 +178,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: bams - readgroups: readgroups + sequence: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/exome_alignment.cwl b/definitions/pipelines/exome_alignment.cwl index 976187eed..bd56f45be 100644 --- a/definitions/pipelines/exome_alignment.cwl +++ b/definitions/pipelines/exome_alignment.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -92,11 +91,10 @@ outputs: outputSource: qc/verify_bam_id_depth steps: alignment: - run: ../subworkflows/bam_to_bqsr.cwl + run: ../subworkflows/sequence_to_bqsr.cwl in: reference: reference - bams: bams - readgroups: readgroups + unaligned: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/gathered_cle_aml_trio.cwl b/definitions/pipelines/gathered_cle_aml_trio.cwl index b02265c1b..761392e83 100644 --- a/definitions/pipelines/gathered_cle_aml_trio.cwl +++ b/definitions/pipelines/gathered_cle_aml_trio.cwl @@ -7,28 +7,23 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' - followup_bams: - type: File[] - followup_readgroups: - type: string[] + followup_sequence: + type: ../types/sequence_data.yml#sequence_data[] followup_name: type: string? default: 'followup' @@ -189,14 +184,11 @@ steps: run: cle_aml_trio.cwl in: reference: reference - tumor_bams: tumor_bams - tumor_readgroups: tumor_readgroups + tumor_sequence: tumor_sequence tumor_name: tumor_name - normal_bams: normal_bams - normal_readgroups: normal_readgroups + normal_sequence: normal_sequence normal_name: normal_name - followup_bams: followup_bams - followup_readgroups: followup_readgroups + followup_sequence: followup_sequence followup_name: followup_name mills: mills known_indels: known_indels diff --git a/definitions/pipelines/gathered_cle_somatic_exome.cwl b/definitions/pipelines/gathered_cle_somatic_exome.cwl index 9a70899db..e8e713cb8 100644 --- a/definitions/pipelines/gathered_cle_somatic_exome.cwl +++ b/definitions/pipelines/gathered_cle_somatic_exome.cwl @@ -7,21 +7,18 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_cram_name: type: string? default: 'tumor.cram' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_cram_name: type: string? default: 'normal.cram' @@ -152,11 +149,9 @@ steps: run: cle_somatic_exome.cwl in: reference: reference - tumor_bams: tumor_bams - tumor_readgroups: tumor_readgroups + tumor_sequence: tumor_sequence tumor_cram_name: tumor_cram_name - normal_bams: normal_bams - normal_readgroups: normal_readgroups + normal_sequence: normal_sequence normal_cram_name: normal_cram_name mills: mills known_indels: known_indels diff --git a/definitions/pipelines/gathered_somatic_exome.cwl b/definitions/pipelines/gathered_somatic_exome.cwl index 6d12c42ad..0d1e6f56d 100644 --- a/definitions/pipelines/gathered_somatic_exome.cwl +++ b/definitions/pipelines/gathered_somatic_exome.cwl @@ -7,21 +7,18 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_cram_name: type: string? default: 'tumor.cram' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_cram_name: type: string? default: 'normal.cram' @@ -149,11 +146,9 @@ steps: run: somatic_exome.cwl in: reference: reference - tumor_bams: tumor_bams - tumor_readgroups: tumor_readgroups + tumor_sequence: tumor_sequence tumor_cram_name: tumor_cram_name - normal_bams: normal_bams - normal_readgroups: normal_readgroups + normal_sequence: normal_sequence normal_cram_name: normal_cram_name mills: mills known_indels: known_indels diff --git a/definitions/pipelines/germline_exome.cwl b/definitions/pipelines/germline_exome.cwl index 3103c8e95..0ad178adc 100644 --- a/definitions/pipelines/germline_exome.cwl +++ b/definitions/pipelines/germline_exome.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -153,8 +152,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: bams - readgroups: readgroups + sequence: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/germline_exome_hla_typing.cwl b/definitions/pipelines/germline_exome_hla_typing.cwl index a610f5c16..b0e0be618 100644 --- a/definitions/pipelines/germline_exome_hla_typing.cwl +++ b/definitions/pipelines/germline_exome_hla_typing.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -149,8 +148,7 @@ steps: run: germline_exome.cwl in: reference: reference - bams: bams - readgroups: readgroups + sequence: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/germline_wgs.cwl b/definitions/pipelines/germline_wgs.cwl index fb35e969e..5e6801be6 100644 --- a/definitions/pipelines/germline_wgs.cwl +++ b/definitions/pipelines/germline_wgs.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -263,8 +262,7 @@ steps: run: wgs_alignment.cwl in: reference: reference - bams: bams - readgroups: readgroups + sequence: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index 689bc42fa..ced9d2569 100644 --- a/definitions/pipelines/immuno.cwl +++ b/definitions/pipelines/immuno.cwl @@ -7,6 +7,7 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: #rnaseq inputs @@ -53,17 +54,13 @@ inputs: #somatic inputs reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' @@ -641,11 +638,9 @@ steps: run: somatic_exome.cwl in: reference: reference - tumor_bams: tumor_bams - tumor_readgroups: tumor_readgroups + tumor_sequence: tumor_sequence tumor_name: tumor_name - normal_bams: normal_bams - normal_readgroups: normal_readgroups + normal_sequence: normal_sequence normal_name: normal_name mills: mills known_indels: known_indels @@ -699,8 +694,7 @@ steps: run: germline_exome_hla_typing.cwl in: reference: reference - bams: normal_bams - readgroups: normal_readgroups + sequence: normal_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/somatic_exome.cwl b/definitions/pipelines/somatic_exome.cwl index cf6380eb7..1c80978b2 100644 --- a/definitions/pipelines/somatic_exome.cwl +++ b/definitions/pipelines/somatic_exome.cwl @@ -7,21 +7,18 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: reference: string - tumor_bams: - type: File[] - tumor_readgroups: - type: string[] + tumor_sequence: + type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' - normal_bams: - type: File[] - normal_readgroups: - type: string[] + normal_sequence: + type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' @@ -353,8 +350,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: tumor_bams - readgroups: tumor_readgroups + sequence: tumor_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf @@ -377,8 +373,7 @@ steps: run: exome_alignment.cwl in: reference: reference - bams: normal_bams - readgroups: normal_readgroups + sequence: normal_sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/wgs.cwl b/definitions/pipelines/wgs.cwl index 348db2102..6f401bf0e 100644 --- a/definitions/pipelines/wgs.cwl +++ b/definitions/pipelines/wgs.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -154,8 +153,7 @@ steps: run: wgs_alignment.cwl in: reference: reference - bams: bams - readgroups: readgroups + sequence: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/definitions/pipelines/wgs_alignment.cwl b/definitions/pipelines/wgs_alignment.cwl index fcb1ebfd5..60a8e6814 100644 --- a/definitions/pipelines/wgs_alignment.cwl +++ b/definitions/pipelines/wgs_alignment.cwl @@ -7,13 +7,12 @@ requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml + - $import: ../types/sequence_data.yml - class: SubworkflowFeatureRequirement inputs: reference: string - bams: - type: File[] - readgroups: - type: string[] + sequence: + type: ../types/sequence_data.yml#sequence_data[] mills: type: File secondaryFiles: [.tbi] @@ -99,11 +98,10 @@ outputs: outputSource: qc/bamcoverage_bigwig steps: alignment: - run: ../subworkflows/bam_to_bqsr.cwl + run: ../subworkflows/sequence_to_bqsr.cwl in: reference: reference - bams: bams - readgroups: readgroups + unaligned: sequence mills: mills known_indels: known_indels dbsnp_vcf: dbsnp_vcf diff --git a/example_data/cle_IDT_somatic_exome_template.yaml b/example_data/cle_IDT_somatic_exome_template.yaml index f44a6f2c4..0b7cb3851 100644 --- a/example_data/cle_IDT_somatic_exome_template.yaml +++ b/example_data/cle_IDT_somatic_exome_template.yaml @@ -54,11 +54,12 @@ varscan_strand_filter: 1 varscan_min_var_freq: 0.08 varscan_p_value: 0.1 varscan_max_normal_freq: 0.1 -normal_bams: -- class: File - path: NORMAL_BAM_PATH -normal_readgroups: -- "NORMAL_RG_STR" +normal_sequence: + - sequence: + bam: + class: File + path: NORMAL_BAM_PATH + readgroup: "NORMAL_RG_STR" omni_vcf: class: File path: /gscmnt/gc2709/info/production_reference_GRCh38DH/accessory_vcf/omni25-ld-pruned-20000-2000-0.5-annotated.wchr.sites_only.b38.autosomes_only.vcf.gz @@ -76,11 +77,12 @@ synonyms_file: target_intervals: class: File path: /gscmnt/gc2709/info/production_reference_GRCh38DH/CLE/IDTExome/xgen-exome-research-panel-targets.interval_list -tumor_bams: -- class: File - path: TUMOR_BAM_PATH -tumor_readgroups: -- "TUMOR_RG_STR" +tumor_sequence: + - sequence: + bam: + class: File + path: TUMOR_BAM_PATH + readgroup: "TUMOR_RG_STR" filter_docm_variants: true filter_minimum_depth: 20 cle_vcf_filter: true diff --git a/example_data/cle_aml_trio_template.yaml b/example_data/cle_aml_trio_template.yaml index 232d0f46b..898655c59 100644 --- a/example_data/cle_aml_trio_template.yaml +++ b/example_data/cle_aml_trio_template.yaml @@ -87,11 +87,12 @@ varscan_strand_filter: 1 varscan_min_var_freq: 0.08 varscan_p_value: 0.1 varscan_max_normal_freq: 0.1 -normal_bams: -- class: File - path: NORMAL_BAM_PATH -normal_readgroups: -- "NORMAL_RG_STR" +normal_sequence: + - sequence: + bam: + class: File + path: NORMAL_BAM_PATH + readgroup: "NORMAL_RG_STR" omni_vcf: class: File path: /gscmnt/gc2709/info/production_reference_GRCh38DH/accessory_vcf/omni25-ld-pruned-20000-2000-0.5-annotated.wchr.sites_only.b38.autosomes_only.vcf.gz @@ -116,16 +117,18 @@ synonyms_file: target_intervals: class: File path: /gscmnt/gc13016/cle/54f8f7b915cb472aa183c721307369ab_scratch_space/new_AML_trio/new_cwl/bed_file/IDT_targets_plus50bp_build38.resorted.merged.interval_list -tumor_bams: -- class: File - path: TUMOR_BAM_PATH -tumor_readgroups: -- "TUMOR_RG_STR" -followup_bams: -- class: File - path: FOLLOWUP_BAM_PATH -followup_readgroups: -- "FOLLOWUP_RG_STR" +tumor_sequence: + - sequence: + bam: + class: File + path: TUMOR_BAM_PATH + readgroup: "TUMOR_RG_STR" +followup_sequence: + - sequence: + bam: + class: File + path: FOLLOWUP_BAM_PATH + readgroup: "FOLLOWUP_RG_STR" filter_docm_variants: false filter_minimum_depth: 20 annotate_coding_only: false diff --git a/example_data/exome_workflow.yaml b/example_data/exome_workflow.yaml index d96ff75e5..ae3ae7175 100644 --- a/example_data/exome_workflow.yaml +++ b/example_data/exome_workflow.yaml @@ -2,11 +2,6 @@ bait_intervals: class: File path: exome_workflow/chr17_test_bait.interval_list -bams: -- class: File - path: exome_workflow/2895499223.bam -- class: File - path: exome_workflow/2895499237.bam bqsr_intervals: - chr17 custom_gnomad_vcf: @@ -40,11 +35,19 @@ per_target_intervals: class: File path: exome_workflow/chr17_test_target.interval_list picard_metric_accumulation_level: ALL_READS -readgroups: -- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" -- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" reference: /gscmnt/gc2764/cad/jwalker/toil_test/cancer-genomics-workflow/example_data/exome_workflow/chr17_test.fa sample_name: H_NJ-HCC1395-HCC1395 +sequence: + - sequence: + bam: + class: File + path: exome_workflow/2895499223.bam + readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" + - sequence: + bam: + class: File + path: exome_workflow/2895499237.bam + readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" synonyms_file: class: File path: exome_workflow/chromAlias.ensembl.txt diff --git a/example_data/germline_exome.yaml b/example_data/germline_exome.yaml index f1ccc9ab8..c789dbff1 100644 --- a/example_data/germline_exome.yaml +++ b/example_data/germline_exome.yaml @@ -2,11 +2,6 @@ bait_intervals: class: File path: exome_workflow/chr17_test_bait.interval_list -bams: -- class: File - path: exome_workflow/2895499223.bam -- class: File - path: exome_workflow/2895499237.bam bqsr_intervals: - chr17 custom_gnomad_vcf: @@ -47,10 +42,18 @@ summary_intervals: class: File path: exome_workflow/chr17_test_genes.interval_list picard_metric_accumulation_level: ALL_READS -readgroups: -- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" -- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" reference: "/gscmnt/gc2764/cad/jgarza/shared/exome_workflow/chr17_test.fa" +sequence: + - sequence: + bam: + class: File + path: exome_workflow/2895499223.bam + readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" + - sequence: + bam: + class: File + path: exome_workflow/2895499237.bam + readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" synonyms_file: class: File path: exome_workflow/chromAlias.ensembl.txt diff --git a/example_data/germline_wgs.yaml b/example_data/germline_wgs.yaml index 4ae5b7e6d..42b2b4433 100644 --- a/example_data/germline_wgs.yaml +++ b/example_data/germline_wgs.yaml @@ -1,9 +1,4 @@ --- -bams: -- class: File - path: exome_workflow/2895499223.bam -- class: File - path: exome_workflow/2895499237.bam bqsr_intervals: ["chr17"] custom_gnomad_vcf: class: File @@ -32,9 +27,17 @@ qc_intervals: class: File path: exome_workflow/chr17_test_bait.interval_list reference: "/gscmnt/gc2764/cad/jgarza/pipeline_data/exome_workflow/chr17_test.fa" -readgroups: -- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" -- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" +sequence: + - sequence: + bam: + class: File + path: exome_workflow/2895499223.bam + readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" + - sequence: + bam: + class: File + path: exome_workflow/2895499237.bam + readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" summary_intervals: [ {label: "genes", file: { class: File, path: 'exome_workflow/chr17_test_genes.interval_list' }} ] synonyms_file: diff --git a/example_data/somatic_exome.yaml b/example_data/somatic_exome.yaml index 49619cfb8..856d12bf2 100644 --- a/example_data/somatic_exome.yaml +++ b/example_data/somatic_exome.yaml @@ -2,22 +2,28 @@ bait_intervals: class: File path: exome_workflow/chr17_test_bait.interval_list -tumor_bams: -- class: File - path: exome_workflow/2895499223.bam -- class: File - path: exome_workflow/2895499237.bam -tumor_readgroups: -- "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" -- "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" -normal_bams: -- class: File - path: exome_workflow/2895499331.bam -- class: File - path: exome_workflow/2895499399.bam -normal_readgroups: -- "@RG\tID:2895499331\tPU:H7HY2CCXX.3.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC" -- "@RG\tID:2895499399\tPU:H7HY2CCXX.4.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC" +tumor_sequence: + - sequence: + bam: + class: File + path: exome_workflow/2895499223.bam + readgroup: "@RG\tID:2895499223\tPU:H7HY2CCXX.3.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" + - sequence: + bam: + class: File + path: exome_workflow/2895499237.bam + readgroup: "@RG\tID:2895499237\tPU:H7HY2CCXX.4.ATCACGGT\tSM:H_NJ-HCC1395-HCC1395\tLB:H_NJ-HCC1395-HCC1395-lg24-lib1\tPL:Illumina\tCN:WUGSC" +normal_sequence: + - sequence: + bam: + class: File + path: exome_workflow/2895499331.bam + readgroup: "@RG\tID:2895499331\tPU:H7HY2CCXX.3.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC" + - sequence: + bam: + class: File + path: exome_workflow/2895499399.bam + readgroup: "@RG\tID:2895499399\tPU:H7HY2CCXX.4.TGACCACG\tSM:H_NJ-HCC1395-HCC1395_BL\tLB:H_NJ-HCC1395-HCC1395_BL-lg21-lib1\tPL:Illumina\tCN:WUGSC" custom_gnomad_vcf: class: File path: exome_workflow/chr17_test_gnomADe.vcf.gz From b2b638daa11c995e847e0604213bf67ecc826598 Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Mon, 22 Jul 2019 19:02:41 -0500 Subject: [PATCH 5/6] Use an adapter to circumvent issues in staging files. --- definitions/subworkflows/sequence_to_bqsr.cwl | 2 +- definitions/tools/sequence_align_and_tag.cwl | 30 +++++++------ .../tools/sequence_align_and_tag_adapter.cwl | 44 +++++++++++++++++++ 3 files changed, 62 insertions(+), 14 deletions(-) create mode 100644 definitions/tools/sequence_align_and_tag_adapter.cwl diff --git a/definitions/subworkflows/sequence_to_bqsr.cwl b/definitions/subworkflows/sequence_to_bqsr.cwl index d8af8dfda..0b8ba5bec 100644 --- a/definitions/subworkflows/sequence_to_bqsr.cwl +++ b/definitions/subworkflows/sequence_to_bqsr.cwl @@ -42,7 +42,7 @@ steps: align: scatter: [unaligned] scatterMethod: dotproduct - run: ../tools/sequence_align_and_tag.cwl + run: ../tools/sequence_align_and_tag_adapter.cwl in: unaligned: unaligned reference: reference diff --git a/definitions/tools/sequence_align_and_tag.cwl b/definitions/tools/sequence_align_and_tag.cwl index 151a12aa0..0c7eef622 100644 --- a/definitions/tools/sequence_align_and_tag.cwl +++ b/definitions/tools/sequence_align_and_tag.cwl @@ -3,7 +3,7 @@ cwlVersion: v1.0 class: CommandLineTool label: "align with bwa_mem and tag" - +doc: "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl to call this" baseCommand: ["/bin/bash", "sequence_alignment_helper.sh"] requirements: - class: SchemaDefRequirement @@ -14,7 +14,6 @@ requirements: ramMin: 20000 - class: DockerRequirement dockerPull: "mgibio/alignment_helper-cwl:1.0.0" - - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement listing: - entryname: 'sequence_alignment_helper.sh' @@ -60,18 +59,23 @@ arguments: - valueFrom: $(runtime.cores) position: 5 prefix: '-n' - - valueFrom: "$(inputs.unaligned.sequence.hasOwnProperty('bam')? inputs.unaligned.sequence.bam : null)" - prefix: '-b' - - valueFrom: "$(inputs.unaligned.sequence.hasOwnProperty('fastq1')? inputs.unaligned.sequence.fastq1 : null)" - prefix: '-1' - - valueFrom: "$(inputs.unaligned.sequence.hasOwnProperty('fastq2')? inputs.unaligned.sequence.fastq2 : null)" - prefix: '-2' - - valueFrom: $(inputs.unaligned.readgroup) - prefix: '-g' inputs: - unaligned: - type: ../types/sequence_data.yml#sequence_data - doc: "the unaligned sequence data with readgroup information" + bam: + type: File? + inputBinding: + prefix: '-b' + fastq1: + type: File? + inputBinding: + prefix: '-1' + fastq2: + type: File? + inputBinding: + prefix: '-2' + readgroup: + type: string + inputBinding: + prefix: '-g' reference: type: string inputBinding: diff --git a/definitions/tools/sequence_align_and_tag_adapter.cwl b/definitions/tools/sequence_align_and_tag_adapter.cwl new file mode 100644 index 000000000..1063aab26 --- /dev/null +++ b/definitions/tools/sequence_align_and_tag_adapter.cwl @@ -0,0 +1,44 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.0 +class: Workflow +label: "adapter for sequence_align_and_tag" +doc: "Some workflow engines won't stage files in our nested structure, so parse it out here" +requirements: + - class: InlineJavascriptRequirement + - class: SchemaDefRequirement + types: + - $import: ../types/sequence_data.yml + - class: StepInputExpressionRequirement + - class: SubworkflowFeatureRequirement +inputs: + unaligned: + type: ../types/sequence_data.yml#sequence_data + doc: "the unaligned sequence data with readgroup information" + reference: + type: string + doc: 'bwa-indexed reference file' +outputs: + aligned_bam: + type: File + outputSource: align_and_tag/aligned_bam +steps: + align_and_tag: + run: sequence_align_and_tag.cwl + in: + reference: reference + bam: + source: unaligned + valueFrom: "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)" + fastq1: + source: unaligned + valueFrom: "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)" + fastq2: + source: unaligned + valueFrom: "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" + readgroup: + source: unaligned + valueFrom: $(self.readgroup) + + out: + [aligned_bam] From 398f7da1ddbac07ea9e8be7b1d7e494492125cbd Mon Sep 17 00:00:00 2001 From: "Thomas B. Mooney" Date: Thu, 1 Aug 2019 19:21:20 +0000 Subject: [PATCH 6/6] Move adapter under subworkflows. --- .../{tools => subworkflows}/sequence_align_and_tag_adapter.cwl | 2 +- definitions/subworkflows/sequence_to_bqsr.cwl | 2 +- definitions/tools/sequence_align_and_tag.cwl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename definitions/{tools => subworkflows}/sequence_align_and_tag_adapter.cwl (96%) diff --git a/definitions/tools/sequence_align_and_tag_adapter.cwl b/definitions/subworkflows/sequence_align_and_tag_adapter.cwl similarity index 96% rename from definitions/tools/sequence_align_and_tag_adapter.cwl rename to definitions/subworkflows/sequence_align_and_tag_adapter.cwl index 1063aab26..f839ad013 100644 --- a/definitions/tools/sequence_align_and_tag_adapter.cwl +++ b/definitions/subworkflows/sequence_align_and_tag_adapter.cwl @@ -24,7 +24,7 @@ outputs: outputSource: align_and_tag/aligned_bam steps: align_and_tag: - run: sequence_align_and_tag.cwl + run: ../tools/sequence_align_and_tag.cwl in: reference: reference bam: diff --git a/definitions/subworkflows/sequence_to_bqsr.cwl b/definitions/subworkflows/sequence_to_bqsr.cwl index 0b8ba5bec..aa9b81bbe 100644 --- a/definitions/subworkflows/sequence_to_bqsr.cwl +++ b/definitions/subworkflows/sequence_to_bqsr.cwl @@ -42,7 +42,7 @@ steps: align: scatter: [unaligned] scatterMethod: dotproduct - run: ../tools/sequence_align_and_tag_adapter.cwl + run: sequence_align_and_tag_adapter.cwl in: unaligned: unaligned reference: reference diff --git a/definitions/tools/sequence_align_and_tag.cwl b/definitions/tools/sequence_align_and_tag.cwl index 0c7eef622..0f9deadc7 100644 --- a/definitions/tools/sequence_align_and_tag.cwl +++ b/definitions/tools/sequence_align_and_tag.cwl @@ -3,7 +3,7 @@ cwlVersion: v1.0 class: CommandLineTool label: "align with bwa_mem and tag" -doc: "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl to call this" +doc: "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" baseCommand: ["/bin/bash", "sequence_alignment_helper.sh"] requirements: - class: SchemaDefRequirement