Maxime U Garcia

Important! Template update for nf-core/tools v3.4.1

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Replaces: - #287 - #290 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added...

### Description of feature - [ ] fix nf-core pipelines warnings - [ ] rescue all functionalities from samplesheet_check - [ ] convert tests

WIP: advisory for snpeff

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@netlify /advisories/snpeff_change_location

For improvment of hello nf-core training: - https://github.com/nf-core/modules/blob/master/modules/nf-core/cowpy/main.nf - https://github.com/nf-core/modules/blob/master/modules/nf-core/cat/cat/main.nf

Release 1.2.2

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Waiting on: - https://github.com/nf-core/rnavar/pull/245 - https://github.com/nf-core/rnavar/pull/249 - https://github.com/nf-core/rnavar/pull/250 - https://github.com/nf-core/rnavar/pull/251 - https://github.com/nf-core/rnavar/pull/253 - https://github.com/nf-core/rnavar/pull/252 - https://github.com/nf-core/rnavar/pull/247 ## PR checklist - [ ] This comment contains a description of changes (with...

Please check in a future PR if this was needed _Originally posted by @maxulysse in https://github.com/nf-core/rnavar/pull/224#discussion_r2298106847_

Nextflow 25.07.0-edge fails with workflow.trace

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Error message since switching to the latest edge release, on pipeline tests when using workflow.trace: `java.lang.RuntimeException: Error: Tracing is disabled. `workflow.trace` is not supported.` Also other warnings are displayed on...

improve tests suite

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

Investigating potential mutect2 filter bug

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

Improve cnvkit tumor_only mode

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> tumor_only mode does not need fasta & target > instead a pre-computed reference.cnn may be supplied which is built from fasta & target out of this PR scope _Originally...