/
bisulfite_qc.cwl
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bisulfite_qc.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Bisulfite QC tools"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
vcf:
type: File
bam:
type: File
reference:
type: string
QCannotation:
type: File
output_dir:
type: string?
default: bisulfite_QC
outputs:
QC_directory:
type: Directory
outputSource: gather_to_sub_directory/gathered_directory
steps:
bisulfite_conversion:
run: ../tools/bisulfite_qc_conversion.cwl
in:
vcf: vcf
bam: bam
reference: reference
QCannotation: QCannotation
out:
[base_convertion, read_convertion, cph_retention, cpg_retention]
mapping_summary:
run: ../tools/bisulfite_qc_mapping_summary.cwl
in:
vcf: vcf
bam: bam
reference: reference
QCannotation: QCannotation
out:
[strand_table, mapping_quality]
cpg_retention_distribution:
run: ../tools/bisulfite_qc_cpg_retention_distribution.cwl
in:
vcf: vcf
bam: bam
reference: reference
QCannotation: QCannotation
out:
[cpg_retention_dist]
coverage_stats:
run: ../tools/bisulfite_qc_coverage_stats.cwl
in:
vcf: vcf
bam: bam
reference: reference
QCannotation: QCannotation
out:
[bga_bed, cov_dist, bga_bed_dup, dup_report, cpg_bed, cov_dist_cpg, cpg_dist]
gather_to_sub_directory:
run: ../tools/gather_to_sub_directory.cwl
in:
outdir: output_dir
files: [bisulfite_conversion/base_convertion, bisulfite_conversion/read_convertion, bisulfite_conversion/cph_retention, bisulfite_conversion/cpg_retention, mapping_summary/strand_table, mapping_summary/mapping_quality, cpg_retention_distribution/cpg_retention_dist, coverage_stats/bga_bed, coverage_stats/cov_dist, coverage_stats/bga_bed_dup, coverage_stats/dup_report, coverage_stats/cpg_bed, coverage_stats/cov_dist_cpg, coverage_stats/cpg_dist]
out:
[gathered_directory]