snpeff and vep - multiqc_files topics #9677
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
11 tasks
nvnieuwk
reviewed
Jan 16, 2026
maxulysse
changed the title
nvnieuwk
approved these changes
Jan 20, 2026
Contributor
nvnieuwk
left a comment
nvnieuwk
left a comment
There was a problem hiding this comment.
Allright LGTM, annotating the tool with it makes sense
delfiterradas
pushed a commit
to delfiterradas/modules
that referenced
this pull request
Jan 20, 2026
* snapshots * fix meta + snapshots * reports-> multiqc_files * add task.process * fix snapshots
github-merge-queue bot
pushed a commit
that referenced
this pull request
Jan 20, 2026
* Emit both png and pdf plots * Update stub test * Update `meta.yml` * Remove trailing whitespace * Correct meta.yml * fix(mitohifi): Update mitohifi to topic versions, add log, and tweak module operation (#9698) fix(mitohifi): update mitohifi to version topics, add a log file output, and change input processing to allow multiple input files * Samtools update nf35 (#9699) * Update seqtk/* version number collection for nf-core 3.5 * Update seqtk/* version number collection in subworkflows for nf-core 3.5 * Changed code for adjusting 3.5.0 * Changed code for adjusting 3.5.0 * Due to changes in /tseemann/barrnap * changed expression in version detection sed $(git grep -l grep) -i -e "s/grep Version | //" -e "s/ sed/ sed -n/" -e"s/Version/^Version/" -e"s,sion: //,sion: //p," * updated snapshot of fasta_hmmsearch_rank_fastas * Update samtools/bgzip version number collection for nf-core 3.5 --------- Co-authored-by: Takii-Fujita <[email protected]> Co-authored-by: Charles Plessy <[email protected]> * Update CHECKM2_PREDICT to allow more flexible pickup of database file (#9691) * Add new input channel for premade seqid2map file * Add extra tests for using custom seqid2map file * Apply suggestions from code review * Update modules/nf-core/kraken2/build/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Allow more flexible database input using `find` to locate dmnd file * Replace broken download module with NXF download and untar * Also replace galah test * Fix path to script * Update main.nf.test * Update modules/nf-core/checkm2/predict/tests/main.nf.test * Update modules/nf-core/galah/tests/main.nf.test * Fix test code --------- Co-authored-by: Simon Pearce <[email protected]> * strict syntax + versions topic (#9693) * strict syntax + versions topic * simplified eval for versions and added ontologies * snpeff and vep - multiqc_files topics (#9677) * snapshots * fix meta + snapshots * reports-> multiqc_files * add task.process * fix snapshots * Update/local cd search (#9696) * Update container image URL for localcdsearch * Update container URL for localcdsearch module * Samtools quickcheck (#9678) * initial stage commit for samtools quickcheck * fix tests * update tests * fix meta * changed module objective: returns exit code env * fix linter shenanigans * change description of EXIT_CODE return type * more negative tests * correcting Bad header test case * adding htslib for good practice * Fix `abundance_differential_filter` to only generate one normalized matrix with `dream` (#9675) * Bugfix: Generate dream normalised matrix only once * Update snapshot * Voom can only work with 1 thread * Fix parallel execution of voom * Fix ext.when configuration * Remove `ext.when` declarations * Update png output --------- Co-authored-by: Jim Downie <[email protected]> Co-authored-by: takiifujita-ui <[email protected]> Co-authored-by: Takii-Fujita <[email protected]> Co-authored-by: Charles Plessy <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Evangelos Karatzas <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Alejandra Escobar <[email protected]> Co-authored-by: Thomas Krannich <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
To just simplify the publication of files via workflow output that are not used in downstream process in pipelines (ie generally fed to multiqc via reports)
cf nf-core/rnavar#277
PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda