Add GRIDSS variant calling #185
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yashpatel6
approved these changes
Nov 15, 2024
config/template.config
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| @@ -16,6 +16,7 @@ params { | |||
| // GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed | |||
| gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed" | |||
| gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta" | |||
| other_jvm_heap = 4.GB | |||
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suggestion: Let's move this to default.config and document it in the README; typically users won't need to change it so it can live in default and user can add it if they need to change it
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Description
Add GRIDSS variant calling step
Closes #178
Testing Results
Checklist
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CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
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algorithm = ['delly', 'manta']. The paths to the test config files and output directories are attached above.