added indexcov : finding large INDEL using the BAI index #1613
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This PR is against the
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OK, I merged into |
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I think it ok now, nevertheless there is still a pre-commit error but I don't understand the error. |
prettier is complaining about the following files: |
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@asp8200 Thanks, yes I saw this, but was is the error exactly ? |
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You can run @nf-core-bot fix linting |
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@nf-core-bot fix linting |
maxulysse
reviewed
Aug 30, 2024
maxulysse
reviewed
Aug 30, 2024
maxulysse
reviewed
Aug 30, 2024
modules/local/indexcov/main.nf
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I would put this in samtools/reindex_bam instead of indexcov
maxulysse
reviewed
Aug 30, 2024
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@maxulysse thank you for the review Maxime, I'm currently away from my code, I'll try to have a look at this next week. Q: this should be set for WGS calling only, what would be the best way/place to set this test ? |
No worries, I know days can be busy
I think I would just allow for it if not using the params.wes, so maybe a message in case tool is used with params, similarly to what we do with other warning messages. |
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@maxulysse back to you, thanks ! |
docs/usage.md
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| @@ -585,11 +585,13 @@ This list is by no means exhaustive and it will depend on the specific analysis | |||
| | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html) | x | x | x | x | x | - | | |||
| | [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | - | x | | |||
| | [Manta](https://github.com/Illumina/manta) | x | x | x | x | x | x | | |||
| | [indexcov](https://github.com/brentp/goleft/tree/master/indexcov) | x | - | x | x | x | x | | |||
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Suggested change
| | [indexcov](https://github.com/brentp/goleft/tree/master/indexcov) | x | - | x | x | x | x | | |
| | [indexcov](https://github.com/brentp/goleft/tree/master/indexcov) | x | - | - | x | - | x | |
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@lindenb From the code it looks like tumor-only is currently not covered. Would remove it here for now
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Going to push this. Need to beat the tools release. Ain't nobody got time for a template update :D
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@nf-core-bot fix linting |
maxulysse
reviewed
Dec 10, 2024
maxulysse
reviewed
Dec 10, 2024
Co-authored-by: Maxime U Garcia <[email protected]>
maxulysse
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Dec 10, 2024
maxulysse
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Dec 10, 2024
docs/sarek_subway.png
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this file should be in the image folder
maxulysse
requested changes
Dec 10, 2024
maxulysse
previously approved these changes
Dec 10, 2024
maxulysse
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Dec 10, 2024
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original discussion: https://nfcore.slack.com/archives/C05V9FRJYMV/p1722884937141779?thread_ts=1696933327.769139&cid=C05V9FRJYMV
nf-core/goleft/indexcov module/subworkflows/local/bam_variant_calling_indexcov/main.nfthe documentation as been brefly updated
(./subworkflows/local/bam_variant_calling_indexcov/main.nf)nf-test test tests/ --verbose --profile +singularityworks./conf/modules/indexcov.configPR checklist
nf-core lint): Too many warnings but nothing related to 'indexcov'nf-test test tests/ --verbose --profile +docker).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated (I'm not sure how to set this without a PR hash...)README.mdis updated (including new tool citations and authors/contributors).