Samtools update nf35 #9699
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Samtools update nf35 #9699
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Refresh snapfile after fixing version issue in subworkflow
sed $(git grep -l grep) -i -e "s/grep Version | //" -e "s/ sed/ sed -n/" -e"s/Version/^Version/" -e"s,sion: //,sion: //p,"
…f_core_modules into seqtk_update_35
charles-plessy
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Jan 20, 2026
delfiterradas
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Jan 20, 2026
* 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 <takahiro-fujita@oist.jp> Co-authored-by: Charles Plessy <charles.plessy@oist.jp>
github-merge-queue bot
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* 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 <takahiro-fujita@oist.jp> Co-authored-by: Charles Plessy <charles.plessy@oist.jp> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <19718667+prototaxites@users.noreply.github.com> Co-authored-by: takiifujita-ui <takiifujita@gmail.com> Co-authored-by: Takii-Fujita <takahiro-fujita@oist.jp> Co-authored-by: Charles Plessy <charles.plessy@oist.jp> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Alejandra Escobar <ales@ebi.ac.uk> Co-authored-by: Thomas Krannich <Krannich479@users.noreply.github.com>
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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