/
harmonization_bwa_mem_no_trim.cwl
103 lines (91 loc) · 2.88 KB
/
harmonization_bwa_mem_no_trim.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
job_uuid: string
interval_bed: File
input_bam: File
reference:
type: File
secondaryFiles: [.fai, .64.amb, .64.ann, .64.bwt, .64.pac, .64.sa, ^.dict, .amb, .ann, .bwt, .pac, .sa]
outputs:
time_metrics_from_bam_to_fastq:
type: File
outputSource: bam_to_fastq/time_metrics
time_metrics_from_bwa_mem_filter_dedup:
type: File[]
outputSource: bwa_mem_filter_dedup/time_metrics
time_metrics_from_merge:
type: File
outputSource: readgroups_merge/time_metrics
time_metrics_from_sort:
type: File
outputSource: bam_sort/time_metrics
time_metrics_from_reheader:
type: File
outputSource: bam_reheader/time_metrics
sorted_bam:
type: File
outputSource: bam_sort/sorted_bam
steps:
get_readgroup_info:
run: ../../tools/harmonization/get_readgroup_name.cwl
in:
bam: input_bam
out: [readgroup_lines, readgroup_names]
bam_to_fastq:
run: ../../tools/harmonization/bam_to_fastq.cwl
in:
job_uuid: job_uuid
readgroup_lines: get_readgroup_info/readgroup_lines
readgroup_names: get_readgroup_info/readgroup_names
filename: input_bam
out: [output_readgroup_lines, output_readgroup_names, output_fastq1, output_fastq2, time_metrics]
bwa_mem_filter_dedup:
run: ../../tools/harmonization/bwa_mem.cwl
scatter: [input_read1_fastq_file, input_read2_fastq_file, readgroup_line, readgroup_name]
scatterMethod: dotproduct
in:
job_uuid: job_uuid
reference: reference
input_read1_fastq_file: bam_to_fastq/output_fastq1
input_read2_fastq_file: bam_to_fastq/output_fastq2
readgroup_line: bam_to_fastq/output_readgroup_lines
readgroup_name: bam_to_fastq/output_readgroup_names
out: [readgroup_bam, time_metrics]
readgroups_merge:
run: ../../tools/harmonization/sambamba_merge.cwl
in:
job_uuid: job_uuid
bams: bwa_mem_filter_dedup/readgroup_bam
base_file_name:
source: job_uuid
valueFrom: $(self)
out: [merged_bam, time_metrics]
get_bam_new_header:
run: ../../tools/harmonization/get_bam_new_header.cwl
in:
bam: readgroups_merge/merged_bam
out: [bam_new_header]
bam_reheader:
run: ../../tools/harmonization/samtools_reheader.cwl
in:
job_uuid: job_uuid
new_header: get_bam_new_header/bam_new_header
interval_bed: interval_bed
bam: readgroups_merge/merged_bam
out: [reheadered_bam, time_metrics]
bam_sort:
run: ../../tools/harmonization/sambamba_sort.cwl
in:
job_uuid: job_uuid
bam: bam_reheader/reheadered_bam
base_file_name:
source: job_uuid
valueFrom: $(self)
out: [sorted_bam, time_metrics]