/
allele-process-reference.cwl
74 lines (57 loc) · 1.65 KB
/
allele-process-reference.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
inputs:
bam_file:
type: File
label: "BAM file"
doc: "BAM file mapped to reference genome"
chrom_length_file:
type: File
label: "Chromosome length file for reference genome"
doc: "Chromosome length file for reference genome"
mapped_reads_number:
type: int
label: "Uniquely mapped reads number"
doc: "Uniquely mapped to reference genome reads number"
output_file_prefix:
type: string
label: "Prefix for all generated output files"
doc: "Corresponds to UID"
threads:
type: int?
default: 2
label: "Number of threads"
doc: "Number of threads for those steps that support multithreading"
outputs:
bambai_pair:
type: File
outputSource: samtools_sort_index/bam_bai_pair
label: "Reference BAM"
doc: "Coordinate sorted BAM file mapped to reference genome"
bigwig_file:
type: File
label: "Reference bigWig file"
doc: "Generated bigWig file for reference genome"
outputSource: bam_to_bigwig/bigwig_file
steps:
samtools_sort_index:
run: ../tools/samtools-sort-index.cwl
in:
sort_input: bam_file
sort_output_filename:
source: output_file_prefix
valueFrom: $(self+".bam")
threads: threads
out: [bam_bai_pair]
bam_to_bigwig:
run: bam-bedgraph-bigwig.cwl
in:
bam_file: samtools_sort_index/bam_bai_pair
chrom_length_file: chrom_length_file
mapped_reads_number: mapped_reads_number
out: [bigwig_file]