Workflow: Subworkflow to allow calling cnvkit with cram instead of bam files

Fetched 2023-01-04 09:40:55 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
access File (Optional)
method String (Optional)
diagram Boolean (Optional)
reference String
tumor_cram File
normal_cram File
scatter_plot Boolean (Optional)
bait_intervals File
drop_low_coverage Boolean (Optional)

Steps

ID Runs Label Doc
run_cnvkit
../tools/cnvkit_batch.cwl (CommandLineTool)
tumor_cram_to_bam
../tools/cram_to_bam.cwl (CommandLineTool)
samtools view cram to bam
normal_cram_to_bam
../tools/cram_to_bam.cwl (CommandLineTool)
samtools view cram to bam

Outputs

ID Type Label Doc
cn_diagram File (Optional)
cn_scatter_plot File (Optional)
intervals_target File (Optional)
reference_coverage File (Optional)
intervals_antitarget File (Optional)
tumor_target_coverage File
normal_target_coverage File
tumor_bin_level_ratios File
tumor_segmented_ratios File
tumor_antitarget_coverage File
normal_antitarget_coverage File
Permalink: https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/subworkflows/cram_to_cnvkit.cwl