🧹 v1.0 release prep #19
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wongjessica93
approved these changes
Jun 13, 2024
migbro
approved these changes
Jun 13, 2024
| return "--tumorBam " + inputs.input_tumor_aligned.path + " --normalBam " + inputs.input_normal_aligned.path + std + mv_cmd; | ||
| } | ||
| } | ||
| /manta-1.4.0.centos6_x86_64/bin/configManta.py --runDir=./ |
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Some nice reorg and cleanup
| $(inputs.input_normal_aligned != null ? inputs.input_tumor_aligned != null ? "--normalBam " + inputs.input_normal_aligned.path : "--bam " + inputs.input_normal_aligned.path : "") | ||
| - position: 10 | ||
| shellQuote: false | ||
| prefix: "&&" |
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prefix: "$$"?! Cue Joe Rogan freaking out GIF
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Description
Prepare the tumor only workflow for release v1.0.0
Change log:
tool_nameoutputs to Manta and ControlFREEC to enable more control in output namingtool_namein output namePart of https://d3b.atlassian.net/browse/BIXU-3679
Type of change
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: