2.0 - #1021
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Dsl2/feature/hrdetect
Germline Maf PublishDir fix
associate errorStrategy with maxRetries
fix tag warning
…ates bugfix for single bam input into MergeBamsAndMarkDuplicates
…lers, to minimize spurious records
…o dsl2/feature/SvABA_BRASS
Dsl2/feature/svaba brass
…andalone process upstream of SomaticMergeSVs
…ded container definition
…_increase Update QcCollectHsMetrics.nf to increase coverage cap
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should we also update the following line in this PR? https://github.com/mskcc/tempo/blob/develop/nextflow.config#L19
as well as nextflowVersion above it?
…tion updated outputs.md
Updated the original PR list to include these missing PRs. |
Updated Nextflow version to 25.04.7 in Travis CI configuration.
…x/travis-ci # Conflicts: # .travis.yml
Migrate CI to GitHub Actions & Fix Tests
Update Nextflow version and pipeline version and switch to Github Actions CI test
Done with #1042 |
…n logic (using empty.json)
Fix CI: Remove oncokb_genes file dependency and use process substitution
| if "MuTect2" in info: | ||
| t_fw = var.samples[tumor]['F1R2'] | ||
| t_rev = var.samples[tumor]['F2R1'] | ||
| n_fw = var.samples[tumor]['F1R2'] |
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Should this be
n_fw = var.samples[normal]['F1R2']
n_rev = var.samples[normal]['F2R1']
Has our strand bias filtering not been working properly?
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i understand how this could be confusing, but there are actually two copies of this script and we should probably consolidate. the script that is actually used is this one: https://github.com/mskcc/tempo/blob/develop/containers/bcftools-vt/filter-vcf.py#L93-L94 and those lines were actually corrected in this script about 5 years ago. the one you're referencing is bcftools-vt-mergesvvcf, in a different folder.
i am not sure i remember exactly the reason i duplicated this folder other than that i was adding mergesvvcf at the time and i think it had some overlapping dependencies with the bcftools-vt container.
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I remember similar discussion before. Not sure it was documented somewhere in other issues. I would leave it this way and reference it somewhere and correct it during the nf-core modules conversion process. Scripts will need to be outside of the container anyway under the new standard I believe.
| doWF_SV = 'sv' in WFs ? true : false | ||
| doWF_facets = doWF_SV && params.assayType == "genome" && ["hisens","purity"].contains(params.svcnv) ? true : doWF_facets | ||
| doWF_loh = ['lohhla', 'snv', 'mutsig'].any(it -> it in WFs) ? true : false | ||
| doWF_SNV = ['snv', 'mutsig'].any(it -> it in WFs) ? true : false ? true : false |
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`
? true : false ? true : false
`
This is unnecessary. We could just have
doWF_SNV = ['snv', 'mutsig'].any { it in WFs }
And it will do the same thing. Not worth holding up release over, just a syntax thing. We will probably just fix it when we move to nf-core style.
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Here is the revised release note for PR #1021 (Tempo v2.0) with the citation marks removed: