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🧹 add toolname to seg out
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dmiller15 committed Jun 13, 2024
1 parent 6f8d76e commit 12a9517
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Showing 2 changed files with 3 additions and 1 deletion.
1 change: 1 addition & 0 deletions subworkflows/kfdrc_controlfreec_sub_wf.cwl
Original file line number Diff line number Diff line change
Expand Up @@ -97,4 +97,5 @@ steps:
ctrlfreec_ratio: control_free_c/ratio
sample_name: input_tumor_name
output_basename: output_basename
tool_name: tool_name
out: [ctrlfreec_ratio2seg]
3 changes: 2 additions & 1 deletion tools/ubuntu_ratio2seg.cwl
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ arguments:
smp = "$(inputs.sample_name)"

ratio_file = open("$(inputs.ctrlfreec_ratio.path)")
out = open("$(inputs.output_basename).controlfreec.seg", "w")
out = open("$(inputs.output_basename).$(inputs.tool_name).seg", "w")
out.write("ID\tchrom\tloc.start\tloc.end\tnum.mark\tseg.mean\n")
head = next(ratio_file)
count = 0
Expand Down Expand Up @@ -70,6 +70,7 @@ inputs:
ctrlfreec_ratio: File
sample_name: string
output_basename: string
tool_name: { type: 'string?', default: "controlfreec", doc: "Tool name to use for output filename" }

outputs:
ctrlfreec_ratio2seg:
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