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02-peakcall.cwl
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class: Workflow
cwlVersion: v1.0
doc: DNase-seq 02 quantification
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
input_bam_format:
default: BAM
doc: 'BAM or BAMPE for single-end and paired-end reads respectively (default: BAM)'
type: string
input_bam_files:
type: File[]
nthreads:
default: 1
type: int
steps:
peak-calling-narrow:
run: ../peak_calling/macs2-callpeak.cwl
in:
extsize:
valueFrom: ${return 200}
bdg:
valueFrom: ${return true}
nomodel:
valueFrom: ${return true}
format: input_bam_format
shift:
valueFrom: ${return -100}
q:
valueFrom: ${return 0.10}
treatment:
source: input_bam_files
valueFrom: $([self])
scatter:
- treatment
out:
- output_peak_file
- output_ext_frag_bdg_file
- output_peak_xls_file
count-reads-filtered:
run: ../peak_calling/count-reads-after-filtering.cwl
in:
peak_xls_file: peak-calling-narrow/output_peak_xls_file
scatter: peak_xls_file
out:
- read_count_file
spp:
run: ../spp/spp.cwl
in:
input_bam: input_bam_files
nthreads: nthreads
savp:
valueFrom: ${return true}
scatterMethod: dotproduct
scatter:
- input_bam
out:
- output_spp_cross_corr
- output_spp_cross_corr_plot
extract-peak-frag-length:
run: ../spp/extract-best-frag-length.cwl
in:
input_spp_txt_file: spp/output_spp_cross_corr
scatter: input_spp_txt_file
out:
- output_best_frag_length
extract-count-reads-in-peaks:
run: ../peak_calling/samtools-extract-number-mapped-reads.cwl
in:
output_suffix:
valueFrom: .read_count.in_peaks.within_reps.txt
input_bam_file: filter-reads-in-peaks/filtered_file
scatter: input_bam_file
out:
- output_read_count
filter-reads-in-peaks:
run: ../peak_calling/samtools-filter-in-bedfile.cwl
in:
input_bam_file: input_bam_files
input_bedfile: peak-calling-narrow/output_peak_file
scatterMethod: dotproduct
scatter:
- input_bam_file
- input_bedfile
out:
- filtered_file
count-peaks:
run: ../utils/count-with-output-suffix.cwl
in:
output_suffix:
valueFrom: .peak_count.within_replicate.txt
input_file: peak-calling-narrow/output_peak_file
scatter: input_file
out:
- output_counts
outputs:
output_filtered_read_count_file:
doc: Filtered read count reported by MACS2
type: File[]
outputSource: count-reads-filtered/read_count_file
output_extended_narrowpeak_file:
doc: peakshift/phantomPeak extended fragment results file
type: File[]
outputSource: peak-calling-narrow/output_ext_frag_bdg_file
output_narrowpeak_file:
doc: peakshift/phantomPeak results file
type: File[]
outputSource: peak-calling-narrow/output_peak_file
output_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: count-peaks/output_counts
output_spp_cross_corr_plot:
doc: peakshift/phantomPeak results file
type: File[]
outputSource: spp/output_spp_cross_corr_plot
output_spp_x_cross_corr:
doc: peakshift/phantomPeak results file
type: File[]
outputSource: spp/output_spp_cross_corr
output_peak_xls_file:
doc: Peak calling report file (*_peaks.xls file produced by MACS2)
type: File[]
outputSource: peak-calling-narrow/output_peak_xls_file
output_read_in_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: extract-count-reads-in-peaks/output_read_count