/
wgs_alignment.cwl
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/
wgs_alignment.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "wgs alignment with qc"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
omni_vcf:
type: File
secondaryFiles: [.tbi]
intervals:
type: File
picard_metric_accumulation_level:
type: string
bqsr_intervals:
type: string[]?
minimum_mapping_quality:
type: int?
minimum_base_quality:
type: int?
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
outputs:
cram:
type: File
outputSource: alignment/final_cram
mark_duplicates_metrics:
type: File
outputSource: alignment/mark_duplicates_metrics_file
insert_size_metrics:
type: File
outputSource: qc/insert_size_metrics
insert_size_histogram:
type: File
outputSource: qc/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: qc/alignment_summary_metrics
gc_bias_metrics:
type: File
outputSource: qc/gc_bias_metrics
gc_bias_metrics_chart:
type: File
outputSource: qc/gc_bias_metrics_chart
gc_bias_metrics_summary:
type: File
outputSource: qc/gc_bias_metrics_summary
wgs_metrics:
type: File
outputSource: qc/wgs_metrics
flagstats:
type: File
outputSource: qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: qc/verify_bam_id_depth
per_base_coverage_metrics:
type: File[]
outputSource: qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: qc/per_base_hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: qc/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: qc/per_target_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: qc/summary_hs_metrics
steps:
alignment:
run: ../subworkflows/bam_to_bqsr.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
out: [final_cram,mark_duplicates_metrics_file]
qc:
run: ../subworkflows/qc_wgs.cwl
in:
cram: alignment/final_cram
reference: reference
omni_vcf: omni_vcf
intervals: intervals
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
out: [insert_size_metrics, insert_size_histogram, alignment_summary_metrics, gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary, wgs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics]