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Update to topics custom/*#11256

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SPPearce merged 22 commits intonf-core:masterfrom
LouisLeNezet:custom
Apr 22, 2026
Merged

Update to topics custom/*#11256
SPPearce merged 22 commits intonf-core:masterfrom
LouisLeNezet:custom

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@LouisLeNezet LouisLeNezet commented Apr 21, 2026

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Closes #10692
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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
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  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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@LouisLeNezet LouisLeNezet self-assigned this Apr 21, 2026
SPPearce
SPPearce reviewed Apr 22, 2026
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Comment thread modules/nf-core/custom/geneticmapconvert/tests/main.nf.test
Comment on lines +17 to +19
params {
geneticmapconvert_args = ""
}
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@SPPearce SPPearce Apr 22, 2026

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What is this doing (all through?)

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@LouisLeNezet LouisLeNezet Apr 22, 2026

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Nextflow was complaning due to access of an undefined params in the config file.
So I simply added an empty one in all test cases that wasn't using one.

SPPearce
SPPearce approved these changes Apr 22, 2026
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Ok, non-standard params name aside.

@SPPearce SPPearce added this pull request to the merge queue Apr 22, 2026
Merged via the queue into nf-core:master with commit c3a7c47 Apr 22, 2026
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pinin4fjords added a commit to nf-core/rnaseq that referenced this pull request Apr 22, 2026
@pinin4fjords @claude
chore: sync custom/catadditionalfasta and rewire prefix/versions
1b4b624 
Upstream nf-core/modules#11256 moved custom/catadditionalfasta to
topic-based versions, made the output prefix controlled by
`task.ext.prefix ?: meta.id`, and fixed outputs to `out/${prefix}.{fasta,gtf}`.

Pipeline-side wiring:

- Drop the manual `.mix(CUSTOM_CATADDITIONALFASTA.out.versions)` so
  versions aren't double-counted alongside the topic.
- Fix the stale `CAT_ADDITIONAL_FASTA` selector in
  conf/modules/prepare_genome.config to `CUSTOM_CATADDITIONALFASTA`,
  and split `PREPROCESS_TRANSCRIPTS_FASTA_GENCODE` into its own block.
- Set `ext.prefix = "${params.genome ?: fasta.baseName}_${add_fasta.baseName}"`
  on `CUSTOM_CATADDITIONALFASTA` to preserve the previous
  `{genome}_{add_name}` output filename (new module default is `meta.id`,
  which would rename outputs to `genome_transcriptome.{fasta,gtf}`).

[skip ci]

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords pinin4fjords mentioned this pull request Apr 22, 2026
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pinin4fjords added a commit to nf-core/rnaseq that referenced this pull request Apr 22, 2026
@pinin4fjords @claude
chore(modules): sync nf-core components and wire catadditionalfasta i…
c6ed232 
…ntegration

Bump to the latest upstream of:

- fq/lint (nf-core/modules#11227): constrain reads arity to 1..2
- ribodetector (nf-core/modules#11258): unpin GPU container from pytorch-gpu=1.11.0; emit cuda version on the topic
- tximeta/tximport (nf-core/modules#11141): fix gene-level crash on mismatched transcript FASTA/GTF
- fastq_fastqc_umitools_trimgalore (nf-core/modules#11228): handle null trim_log in the read-count map
- custom/catadditionalfasta (nf-core/modules#11256): topic-based versions, explicit out/\${prefix}.{fasta,gtf} paths, task.ext.prefix ?: meta.id prefix handling

The custom/catadditionalfasta interface change needs pipeline-side follow-up in conf/modules/prepare_genome.config:

- Fix the stale CAT_ADDITIONAL_FASTA selector (now CUSTOM_CATADDITIONALFASTA) and split PREPROCESS_TRANSCRIPTS_FASTA_GENCODE into its own block.
- Set ext.prefix = "\${params.genome ?: fasta.baseName}_\${add_fasta.baseName}" so output filenames follow the previous {genome}_{add_name} pattern; the new module default (meta.id) would otherwise rename outputs to genome_transcriptome.{fasta,gtf}.

Behaviour note: fixing the withName selector also exposes a pre-existing intent that was masked. CUSTOM_CATADDITIONALFASTA outputs now only publish when --save_reference is set; the stale selector previously let them fall through to the default publishDir and land in <outdir>/custom/out/ regardless of --save_reference.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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