/
bams2gvcf.woBQSR_male.multisamples.cwl
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bams2gvcf.woBQSR_male.multisamples.cwl
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cwlVersion: v1.0
class: Workflow
$namespaces:
edam: 'http://edamontology.org/'
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
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)
nthreads:
type: int
doc: number of cpu cores to be used
inputSamples:
type:
type: array
items:
- type: record
fields:
bam_files:
type: File[]
outprefix:
type: string
chrXY_outprefix:
type: string
steps:
bams2gvcfwoBQSR_male:
run: bams2gvcf.woBQSR_male.cwl
in:
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
inputSamples: inputSamples
bam_files:
valueFrom: $(inputs.inputSamples.bam_files)
outprefix:
valueFrom: $(inputs.inputSamples.outprefix)
chrXY_outprefix:
valueFrom: $(inputs.inputSamples.chrXY_outprefix)
scatter:
- inputSamples
scatterMethod: dotproduct
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
- gatk3_HaplotypeCaller_XCORE_ploidy1_vcf
- gatk3_HaplotypeCaller_XCORE_ploidy1_log
- gatk3_HaplotypeCaller_Y_ploidy1_vcf
- gatk3_HaplotypeCaller_Y_ploidy1_log
- gatk3_SelectVariants_PAR1_vcf
- gatk3_SelectVariants_PAR1_log
- gatk3_SelectVariants_PAR2_vcf
- gatk3_SelectVariants_PAR2_log
- bcftools_concat_vcf
- bcftools_index_vcf_tbi
outputs:
rmdup_bam:
type: File[]
outputSource: bams2gvcfwoBQSR_male/rmdup_bam
secondaryFiles:
- ^.bai
rmdup_metrics:
type: File[]
outputSource: bams2gvcfwoBQSR_male/rmdup_metrics
rmdup_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/rmdup_log
picard_collect_multiple_metrics_alignment_summary_metrics:
type: File[]
outputSource: bams2gvcfwoBQSR_male/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: bams2gvcfwoBQSR_male/picard_collect_multiple_metrics_insert_size_metrics
secondaryFiles:
- ^.insert_size_histogram.pdf
picard_collect_multiple_metrics_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_collect_multiple_metrics_log
samtools_flagstat_flagstat:
type: File[]
outputSource: bams2gvcfwoBQSR_male/samtools_flagstat_flagstat
samtools_idxstats_idxstats:
type: File[]
outputSource: bams2gvcfwoBQSR_male/samtools_idxstats_idxstats
picard_CollectWgsMetrics_autosome_wgs_metrics:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_CollectWgsMetrics_autosome_wgs_metrics
picard_CollectWgsMetrics_autosome_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_CollectWgsMetrics_autosome_log
picard_CollectWgsMetrics_chrX_wgs_metrics:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_CollectWgsMetrics_chrX_wgs_metrics
picard_CollectWgsMetrics_chrX_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_CollectWgsMetrics_chrX_log
picard_CollectWgsMetrics_chrY_wgs_metrics:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_CollectWgsMetrics_chrY_wgs_metrics
picard_CollectWgsMetrics_chrY_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/picard_CollectWgsMetrics_chrY_log
gatk3_HaplotypeCaller_vcf:
type: File[]
format: edam:format_3016
outputSource: bams2gvcfwoBQSR_male/gatk3_HaplotypeCaller_vcf
secondaryFiles:
- .tbi
gatk3_HaplotypeCaller_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_HaplotypeCaller_log
gatk3_HaplotypeCaller_XCORE_ploidy1_vcf:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_HaplotypeCaller_XCORE_ploidy1_vcf
secondaryFiles:
- .tbi
gatk3_HaplotypeCaller_XCORE_ploidy1_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_HaplotypeCaller_XCORE_ploidy1_log
gatk3_HaplotypeCaller_Y_ploidy1_vcf:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_HaplotypeCaller_Y_ploidy1_vcf
secondaryFiles:
- .tbi
gatk3_HaplotypeCaller_Y_ploidy1_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_HaplotypeCaller_Y_ploidy1_log
gatk3_SelectVariants_PAR1_vcf:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_SelectVariants_PAR1_vcf
secondaryFiles:
- .tbi
gatk3_SelectVariants_PAR1_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_SelectVariants_PAR1_log
gatk3_SelectVariants_PAR2_vcf:
type: File[]
format: edam:format_3016
outputSource: bams2gvcfwoBQSR_male/gatk3_SelectVariants_PAR2_vcf
secondaryFiles:
- .tbi
gatk3_SelectVariants_PAR2_log:
type: File[]
outputSource: bams2gvcfwoBQSR_male/gatk3_SelectVariants_PAR2_log
bcftools_concat_vcf:
type: File[]
outputSource: bams2gvcfwoBQSR_male/bcftools_concat_vcf
bcftools_index_vcf_tbi:
type: File[]
outputSource: bams2gvcfwoBQSR_male/bcftools_index_vcf_tbi