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alignment_exome.cwl
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alignment_exome.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment with qc"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- $import: ../types/trimming_options.yml
- class: SubworkflowFeatureRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
trimming:
type:
- ../types/trimming_options.yml#trimming_options
- "null"
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]?
bait_intervals:
type: File
final_name:
type: string?
target_intervals:
type: File
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[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
qc_minimum_mapping_quality:
type: int?
qc_minimum_base_quality:
type: int?
outputs:
bam:
type: File
outputSource: alignment/final_bam
secondaryFiles: [.bai, ^.bai]
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
hs_metrics:
type: File
outputSource: qc/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
per_base_coverage_metrics:
type: File[]
outputSource: qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: qc/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: qc/summary_hs_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
steps:
alignment:
run: ../subworkflows/sequence_to_bqsr.cwl
in:
reference: reference
unaligned: sequence
trimming: trimming
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
final_name: final_name
out: [final_bam,mark_duplicates_metrics_file]
qc:
run: ../subworkflows/qc_exome.cwl
in:
bam: alignment/final_bam
reference: reference
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
out: [insert_size_metrics, insert_size_histogram, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]