Workflow: varscan somatic workflow

Fetched 2020-08-14 16:20:38 GMT
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Inputs

ID Type Title Doc
reference String
p_value Float (Optional)
min_var_freq Float (Optional)
max_normal_freq Float (Optional)
min_coverage Integer (Optional)
normal_bam File
roi_bed File (Optional)
strand_filter Integer (Optional)
tumor_bam File

Steps

ID Runs Label Doc
process_somatic_snvs
../tools/varscan_process_somatic.cwl (CommandLineTool)
varscan v2.4.2 processSomatic
somatic
../tools/varscan_somatic.cwl (CommandLineTool)
varscan v2.4.2 somatic
process_somatic_indels
../tools/varscan_process_somatic.cwl (CommandLineTool)
varscan v2.4.2 processSomatic

Outputs

ID Type Label Doc
indels File
loh_hc_indels File
germline_indels File
loh_snvs File
somatic_indels File
germline_hc_indels File
snvs File
germline_snvs File
somatic_snvs File
loh_hc_snvs File
loh_indels File
somatic_hc_indels File
germline_hc_snvs File
somatic_hc_snvs File
Permalink: https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/subworkflows/varscan.cwl