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waltz-workflow.cwl
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waltz-workflow.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
run_tools:
type:
type: record
fields:
perl_5: string
java_7: string
java_8: string
marianas_path: string
trimgalore_path: string
bwa_path: string
arrg_path: string
picard_path: string
gatk_path: string
abra_path: string
fx_path: string
fastqc_path: string?
cutadapt_path: string?
waltz_path: string
input_bam:
type: File
secondaryFiles: [^.bai]
coverage_threshold: int
gene_list: File
bed_file: File
min_mapping_quality: int
reference_fasta: string
reference_fasta_fai: string
outputs:
pileup:
type: File
outputSource: pileup_metrics/pileup
waltz_output_files:
type: File[]
outputSource: grouped_waltz_files/waltz_files
steps:
count_reads:
run: ../../cwl_tools/waltz/CountReads.cwl
in:
run_tools: run_tools
java_8:
valueFrom: $(inputs.run_tools.java_8)
waltz_path:
valueFrom: $(inputs.run_tools.waltz_path)
input_bam: input_bam
coverage_threshold: coverage_threshold
gene_list: gene_list
bed_file: bed_file
out: [
covered_regions,
fragment_sizes,
read_counts
]
pileup_metrics:
run: ../../cwl_tools/waltz/PileupMetrics.cwl
in:
run_tools: run_tools
java_8:
valueFrom: $(inputs.run_tools.java_8)
waltz_path:
valueFrom: $(inputs.run_tools.waltz_path)
input_bam: input_bam
min_mapping_quality: min_mapping_quality
reference_fasta: reference_fasta
reference_fasta_fai: reference_fasta_fai
bed_file: bed_file
out: [
pileup,
pileup_without_duplicates,
intervals,
intervals_without_duplicates
]
grouped_waltz_files:
run: ../../cwl_tools/expression_tools/group_waltz_files.cwl
in:
covered_regions: count_reads/covered_regions
fragment_sizes: count_reads/fragment_sizes
read_counts: count_reads/read_counts
pileup: pileup_metrics/pileup
pileup_without_duplicates: pileup_metrics/pileup_without_duplicates
intervals: pileup_metrics/intervals
intervals_without_duplicates: pileup_metrics/intervals_without_duplicates
out: [waltz_files]