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bams2gvcf.woBQSR_female.cwl
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bams2gvcf.woBQSR_female.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
id: bam2gvcf-woBQSR-female
label: bam2gvcf-woBQSR-female
cwlVersion: v1.0
$namespaces:
edam: 'http://edamontology.org/'
requirements:
SubworkflowFeatureRequirement: {}
inputs:
reference:
type: File
format: edam:format_1929
doc: FastA file for reference genome
secondaryFiles:
- .fai
- ^.dict
reference_interval_name_autosome:
type: string
default: autosome
doc: interval name for reference genome (autosome)
reference_interval_list_autosome:
type: File
doc: interval list for reference genome (autosome)
reference_interval_name_chrX:
type: string
default: chrX
doc: interval name for reference genome (chrX)
reference_interval_list_chrX:
type: File
doc: interval list for reference genome (chrX)
reference_interval_name_chrY:
type: string
default: chrY
doc: interval name for reference genome (chrY)
reference_interval_list_chrY:
type: File
doc: interval list for reference genome (chrY)
bam_files:
type: File[]
format: edam:format_2572
doc: array of input BAM alignment files (each file should be sorted)
nthreads:
type: int
doc: number of cpu cores to be used
outprefix:
type: string
doc: Output prefix name
steps:
bams2gvcf_woBQSR:
label: bams2gvcf_woBQSR
doc: Call haplotypes from bam files
run: ../Workflows/bams2gvcf.woBQSR.cwl
in:
bam_files: bam_files
outprefix: outprefix
reference: reference
reference_interval_name_autosome: reference_interval_name_autosome
reference_interval_list_autosome: reference_interval_list_autosome
reference_interval_name_chrX: reference_interval_name_chrX
reference_interval_list_chrX: reference_interval_list_chrX
reference_interval_name_chrY: reference_interval_name_chrY
reference_interval_list_chrY: reference_interval_list_chrY
nthreads: nthreads
out:
- rmdup_bam
- rmdup_metrics
- rmdup_log
- picard_collect_multiple_metrics_alignment_summary_metrics
- picard_collect_multiple_metrics_insert_size_metrics
- picard_collect_multiple_metrics_log
- samtools_flagstat_flagstat
- samtools_idxstats_idxstats
- picard_CollectWgsMetrics_autosome_wgs_metrics
- picard_CollectWgsMetrics_autosome_log
- picard_CollectWgsMetrics_chrX_wgs_metrics
- picard_CollectWgsMetrics_chrX_log
- picard_CollectWgsMetrics_chrY_wgs_metrics
- picard_CollectWgsMetrics_chrY_log
- gatk3_HaplotypeCaller_vcf
- gatk3_HaplotypeCaller_log
outputs:
rmdup_bam:
type: File
format: edam:format_2572
outputSource: bams2gvcf_woBQSR/rmdup_bam
secondaryFiles:
- ^.bai
rmdup_metrics:
type: File
outputSource: bams2gvcf_woBQSR/rmdup_metrics
rmdup_log:
type: File
outputSource: bams2gvcf_woBQSR/rmdup_log
picard_collect_multiple_metrics_alignment_summary_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_alignment_summary_metrics
secondaryFiles:
- ^.bait_bias_detail_metrics
- ^.bait_bias_summary_metrics
- ^.base_distribution_by_cycle_metrics
- ^.base_distribution_by_cycle.pdf
- ^.error_summary_metrics
- ^.gc_bias.detail_metrics
- ^.gc_bias.pdf
- ^.gc_bias.summary_metrics
- ^.pre_adapter_detail_metrics
- ^.pre_adapter_summary_metrics
- ^.quality_by_cycle_metrics
- ^.quality_by_cycle.pdf
- ^.quality_distribution_metrics
- ^.quality_distribution.pdf
picard_collect_multiple_metrics_insert_size_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_insert_size_metrics
secondaryFiles:
- ^.insert_size_histogram.pdf
picard_collect_multiple_metrics_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_log
samtools_flagstat_flagstat:
type: File
outputSource: bams2gvcf_woBQSR/samtools_flagstat_flagstat
samtools_idxstats_idxstats:
type: File
outputSource: bams2gvcf_woBQSR/samtools_idxstats_idxstats
picard_CollectWgsMetrics_autosome_wgs_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_autosome_wgs_metrics
picard_CollectWgsMetrics_autosome_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_autosome_log
picard_CollectWgsMetrics_chrX_wgs_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrX_wgs_metrics
picard_CollectWgsMetrics_chrX_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrX_log
picard_CollectWgsMetrics_chrY_wgs_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrY_wgs_metrics
picard_CollectWgsMetrics_chrY_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrY_log
gatk3_HaplotypeCaller_vcf:
type: File
format: edam:format_3016
outputSource: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_vcf
secondaryFiles:
- .tbi
gatk3_HaplotypeCaller_log:
type: File
outputSource: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_log