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chipseq_alignment_mouse.cwl
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chipseq_alignment_mouse.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Chipseq alignment for mouse with qc and creating homer tag directory"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
final_name:
type: string?
chipseq_sequence:
type: ../types/sequence_data.yml#sequence_data[]
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]?
default: []
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]?
default: []
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]?
default: []
picard_metric_accumulation_level:
type: string
minimum_mapping_quality:
type: int?
minimum_base_quality:
type: int?
outputs:
bam:
type: File
outputSource: alignment/final_bam
mark_duplicates_metrics:
type: File
outputSource: alignment/mark_duplicates_metrics_file
tag_directory:
type: Directory
outputSource: homer_tag_directory/tag_directory
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
wgs_metrics:
type: File
outputSource: qc/wgs_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
flagstats:
type: File
outputSource: qc/flagstats
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
summary_hs_metrics:
type: File[]
outputSource: qc/summary_hs_metrics
per_target_hs_metrics:
type: File[]
outputSource: qc/per_target_hs_metrics
bamcoverage_bigwig:
type: File
outputSource: qc/bamcoverage_bigwig
steps:
alignment:
run: ../subworkflows/sequence_to_bqsr_mouse.cwl
in:
reference: reference
unaligned: chipseq_sequence
final_name: final_name
out: [final_bam,mark_duplicates_metrics_file]
bam_to_sam:
run: ../tools/bam_to_sam.cwl
in:
bam: alignment/final_bam
out: [final_sam]
homer_tag_directory:
run: ../tools/homer_tag_directory.cwl
in:
sam: bam_to_sam/final_sam
out: [tag_directory]
qc:
run: ../subworkflows/qc_wgs_mouse.cwl
in:
bam: alignment/final_bam
reference: reference
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,flagstats,per_base_coverage_metrics,per_base_hs_metrics,per_target_coverage_metrics,summary_hs_metrics,per_target_hs_metrics,bamcoverage_bigwig,wgs_metrics]