Release pipeline v1.0.0 #148
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wittyer fixed
plot script fixed
58 test variant extractor for svs
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
…hrough svync input channel is fixed
nvnieuwk
reviewed
Feb 4, 2025
remove conda from checks
nvnieuwk
reviewed
Feb 4, 2025
nvnieuwk
approved these changes
Feb 4, 2025
changes requested by Nicolas
maxulysse
reviewed
Feb 17, 2025
Comment on lines
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| ## [nf-test](https://doi.org/10.1101/2024.05.25.595877) | ||
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| > Forer, L., & Schönherr, S. (2024). Improving the Reliability and Quality of Nextflow Pipelines with nf-test. bioRxiv. https://doi.org/10.1101/2024.05.25.595877 | ||
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| ## [nf-prov](https://github.com/nextflow-io/nf-prov) | ||
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| ## [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) |
update manta_convertinversions
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
copy from fix
maxulysse
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Feb 20, 2025
maxulysse
reviewed
Feb 20, 2025
maxulysse
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maxulysse
reviewed
Feb 20, 2025
modules/local/bgzip/tabix/main.nf
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why not using the nf-core modules?
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I couldnt find a module doing
- check if the input is gzipped
-> if zipped > index
-> if not > zip + index
Please let me know if you know a better way (nft-vcf can be a solution?)
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oh I see, I think I have seen someone trying to add such improvement on a similar modules.
Let's talk about it on the maintainers side
maxulysse
reviewed
Feb 20, 2025
maxulysse
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Feb 20, 2025
maxulysse
reviewed
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maxulysse
reviewed
Feb 20, 2025
apply Maximes changes
maxulysse
reviewed
Feb 21, 2025
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why having the abstract in pdf format and not markdown?
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no specific reason :D I can add as .md, I also send one to ISMB now.
maxulysse
approved these changes
Feb 21, 2025
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).