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checker-workflow-wrapping-workflow.cwl
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checker-workflow-wrapping-workflow.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: MultipleInputFeatureRequirement
inputs:
output_file_basename:
type: string
inputBinding:
position: 10
prefix: --output-file-basename
doc: the basename to use for output files
download_reference_files:
type: string
inputBinding:
position: 11
prefix: --download-reference-files
doc: should we attempt to download the reference files ["true", "false"]
reference_gz_fai:
type: File
inputBinding:
position: 3
prefix: --reference-gz-fai
doc: the reference *.fa.gz.fai file
reference_gz:
type: File
inputBinding:
position: 2
prefix: --reference-gz
doc: the reference *.fa.gz file
reference_gz_pac:
type: File
inputBinding:
position: 7
prefix: --reference-gz-pac
doc: the reference *.fa.gz.pac file
reference_gz_amb:
type: File
inputBinding:
position: 4
prefix: --reference-gz-amb
doc: the reference *.fa.gz.amb file
reads:
type:
type: array
items: File
inputBinding:
position: 1
prefix: --files
reference_gz_bwt:
type: File
inputBinding:
position: 6
prefix: --reference-gz-bwt
doc: the reference *.fa.gz.bwt file
output_dir:
type: string
inputBinding:
position: 9
prefix: --output-dir
doc: the output directory
reference_gz_sa:
type: File
inputBinding:
position: 8
prefix: --reference-gz-sa
doc: the reference *.fa.gz.sa file
reference_gz_ann:
type: File
inputBinding:
position: 5
prefix: --reference-gz-ann
doc: the reference *.fa.gz.ann file
reference_result_normal_bam:
type: File
reference_result_normal_unmapped_bam:
type: File
reference_result_normal_bai:
type: File
reference_result_normal_unmapped_bai:
type: File
reference_result_normal_metrics:
type: File
reference_result_normal_unmapped_metrics:
type: File
outputs:
workflow_output_file:
type: File
outputSource: checker/stdout_log
workflow_err_file:
type: File
outputSource: checker/stderr_log
steps:
pcawg_bwa_mem_aligner:
run: Dockstore.cwl
in:
output_file_basename: output_file_basename
download_reference_files: download_reference_files
reference_gz_fai: reference_gz_fai
reference_gz: reference_gz
reference_gz_pac: reference_gz_pac
reference_gz_amb: reference_gz_amb
reads: reads
reference_gz_bwt: reference_gz_bwt
output_dir: output_dir
reference_gz_sa: reference_gz_sa
reference_gz_ann: reference_gz_ann
out: [
merged_output_bai,
merged_output_unmapped_metrics,
merged_output_bam,
merged_output_metrics,
merged_output_unmapped_bai,
merged_output_unmapped_bam
]
checker:
run: checker/pcawg-bwa-mem-result-checker.cwl
in:
result_files: [
pcawg_bwa_mem_aligner/merged_output_bam,
reference_result_normal_bam,
pcawg_bwa_mem_aligner/merged_output_unmapped_bam,
reference_result_normal_unmapped_bam,
pcawg_bwa_mem_aligner/merged_output_bai,
reference_result_normal_bai,
pcawg_bwa_mem_aligner/merged_output_unmapped_bai,
reference_result_normal_unmapped_bai,
pcawg_bwa_mem_aligner/merged_output_metrics,
reference_result_normal_metrics,
pcawg_bwa_mem_aligner/merged_output_unmapped_metrics,
reference_result_normal_unmapped_metrics
]
out: [stdout_log, stderr_log]