Workflow: varscan somatic workflow

Fetched 2023-01-09 23:01:37 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs reference reference somatic varscan v2.4.2 somatic reference->somatic reference p_value p_value p_value->somatic p_value strand_filter strand_filter strand_filter->somatic strand_filter max_normal_freq max_normal_freq process_somatic_indels varscan v2.4.2 processSomatic max_normal_freq->process_somatic_indels max_normal_freq process_somatic_snvs varscan v2.4.2 processSomatic max_normal_freq->process_somatic_snvs max_normal_freq min_var_freq min_var_freq min_var_freq->somatic min_var_freq normal_cram normal_cram normal_cram->somatic normal_cram min_coverage min_coverage min_coverage->somatic min_coverage tumor_cram tumor_cram tumor_cram->somatic tumor_cram roi_bed roi_bed roi_bed->somatic roi_bed loh_indels loh_indels loh_hc_indels loh_hc_indels somatic_hc_snvs somatic_hc_snvs germline_indels germline_indels loh_hc_snvs loh_hc_snvs germline_snvs germline_snvs indels indels loh_snvs loh_snvs germline_hc_snvs germline_hc_snvs germline_hc_indels germline_hc_indels snvs snvs somatic_snvs somatic_snvs somatic_hc_indels somatic_hc_indels somatic_indels somatic_indels process_somatic_indels->loh_indels process_somatic_indels->loh_hc_indels process_somatic_indels->germline_indels process_somatic_indels->germline_hc_indels process_somatic_indels->somatic_hc_indels process_somatic_indels->somatic_indels process_somatic_snvs->somatic_hc_snvs process_somatic_snvs->loh_hc_snvs process_somatic_snvs->germline_snvs process_somatic_snvs->loh_snvs process_somatic_snvs->germline_hc_snvs process_somatic_snvs->somatic_snvs somatic->indels somatic->snvs somatic->process_somatic_indels variants somatic->process_somatic_snvs variants
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Inputs

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

Steps

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

Outputs

ID Type Label Doc
snvs File
indels File
loh_snvs File
loh_indels File
loh_hc_snvs File
somatic_snvs File
germline_snvs File
loh_hc_indels File
somatic_indels File
germline_indels File
somatic_hc_snvs File
germline_hc_snvs File
somatic_hc_indels File
germline_hc_indels File
Permalink: https://w3id.org/cwl/view/git/e4c851d65f460e8f48ca184120044fce72cb2433/varscan/varscan.cwl