Maxime U Garcia

### Description of feature From @lindenb > Hi All, FYI, in his latest post, Heng Li suggests that minimap2 could be is better at calling variants. > > https://lh3.github.io/2025/04/18/short-rna-seq-read-alignment-with-minimap2

Location of test files created with generate is not parametrisable

1

Following a discussion with @blex-max on the nf-core Slack, I realised that the test files created by the `generate` sub command are at the same location as the `main.nf` they...

For example in https://github.com/nf-core/references/pull/39 I have 2 tests in tests/kallisto.nf.test: - `Run with profile test for kallisto | --input GRCh38_chr21.yml` - `Run with profile test for kallisto | --input assets/genomes/test/pipelines/default_extended.yml`...

Fix issue when lane is 0

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close #1923 Issue was that with lane being `0` was interpreted as `0` the integer, not `0` the string, so the if statement was false. ## PR checklist - [...

Modification from NF Language server

2

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

Need to update this _Originally posted by @maxulysse in https://github.com/nf-core/sarek/pull/1879#discussion_r2068979597_

Provide default UMI/trimming library specific values

1

### Description of feature That would be amazing

POC: Usage for nf-core/references in nf-core/sarek

1

Simplify and improve #1769 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code...

Add check for default outdir to null

2

### Description of feature Example in the cutandrun: https://github.com/nf-core/cutandrun/blob/master/nextflow.config#L116 This params should really be set to null by default. cf https://nfcore.slack.com/archives/C01FKFZ57SA/p1742382940814159

Havin an ssh remote for modules fails linting

1

### Description of the bug When I have this in my `modules.json` `[email protected]:XXX/modules.git`, it fails linting. Switching it to https `https://github.com/XXX/modules.git` solves that issue. ### Command used and terminal output...