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cram_to_cnvkit.cwl
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cram_to_cnvkit.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Subworkflow to allow calling cnvkit with cram instead of bam files"
inputs:
normal_cram:
type: File
secondaryFiles: [^.crai]
tumor_cram:
type: File
secondaryFiles: [^.crai]
reference:
type: string
bait_intervals:
type: File
access:
type: File?
method:
type: string?
diagram:
type: boolean?
scatter_plot:
type: boolean?
drop_low_coverage:
type: boolean?
outputs:
intervals_antitarget:
type: File?
outputSource: run_cnvkit/intervals_antitarget
intervals_target:
type: File?
outputSource: run_cnvkit/intervals_target
normal_antitarget_coverage:
type: File
outputSource: run_cnvkit/normal_antitarget_coverage
normal_target_coverage:
type: File
outputSource: run_cnvkit/normal_target_coverage
reference_coverage:
type: File?
outputSource: run_cnvkit/reference_coverage
cn_diagram:
type: File?
outputSource: run_cnvkit/cn_diagram
cn_scatter_plot:
type: File?
outputSource: run_cnvkit/cn_scatter_plot
tumor_antitarget_coverage:
type: File
outputSource: run_cnvkit/tumor_antitarget_coverage
tumor_target_coverage:
type: File
outputSource: run_cnvkit/tumor_target_coverage
tumor_bin_level_ratios:
type: File
outputSource: run_cnvkit/tumor_bin_level_ratios
tumor_segmented_ratios:
type: File
outputSource: run_cnvkit/tumor_segmented_ratios
steps:
normal_cram_to_bam:
run: ../tools/cram_to_bam.cwl
in:
cram: normal_cram
reference: reference
out:
[bam]
tumor_cram_to_bam:
run: ../tools/cram_to_bam.cwl
in:
cram: tumor_cram
reference: reference
out:
[bam]
run_cnvkit:
run: ../tools/cnvkit_batch.cwl
in:
tumor_bam: tumor_cram_to_bam/bam
normal_bam: normal_cram_to_bam/bam
bait_intervals: bait_intervals
reference: reference
access: access
method: method
diagram: diagram
scatter_plot: scatter_plot
drop_low_coverage: drop_low_coverage
out:
[intervals_antitarget, intervals_target, normal_antitarget_coverage, normal_target_coverage, reference_coverage, cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios]