Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel #9549

Joon-Klaps · 2025-12-10T15:49:10Z

PR checklist

modules/nf-core/cat/cat/tests/main.nf.test.snap

modules/nf-core/cat/cat/main.nf

…cat/cat

…9549) * bump version cat/cat * reinclude cat tags for other modules * patch test name & meta.yml * Update main.nf.test

@mashehu

…9521) * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests * Add ontologies to tcoffee/regressive and upp/align modules (#9484) * add ontologies to tcoffee regressive * add ontologies to upp align * Add module PBMARKDUP (#9457) * Add module pbmarkdup * Fix linting * Update path to test data * Update with code review (--dup-file, log, check file name collisions) * Fix linting * Update path to test data * Update modules/nf-core/pbmarkdup/meta.yml * Fix linting * Enable complex contrast strings in DESeq2 (#9473) * Enable complex contrast strings * Update docker image * Add test case with limma contrast string * Format changes and add test with shrinkage * Declare deepvariant optional html output (#9469) * Add deepvariant optional html * update snapshot * Update modules/nf-core/deepvariant/rundeepvariant/main.nf Co-authored-by: Ramprasad Neethiraj <[email protected]> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <[email protected]> * utils_nfcore_pipeline: fix small lang server error (#9492) fix small lang server error * Fix hisat2/align to support large genome indices (.ht2l) (#9493) HISAT2 uses .ht2l extension instead of .ht2 for large genomes. Updated index detection to match both extensions. Related to nf-core/rnaseq#1643 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude <[email protected]> * Update shinyngs modules to latest release (#9488) * Update semibin/singleeasybin environment (#9495) * add new ontology term to tcoffee align (#9497) * tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (#9489) * Sort file listing so "first" file is deterministic * Declare closure parameter per strict syntax Co-authored-by: Matthias Hörtenhuber <[email protected]> --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> * Sambamba depth add region bed input (#9498) * sambamba add region bed input * fix linting * fix linting * Apply suggestions from code review Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * fix fasta_index_methylseq and fastq_align_dedup workflows (#9496) * fix fasta_index_methylseq and fastq_align_dedup workflows for clarity and consistency - Updated variable names in fasta_index_methylseq to use 'channel' instead of 'Channel' for consistency. - Renamed UNTAR to UNTAR_BISMARK and UNTAR_BWAMETH for clarity in fasta_index_methylseq. - Enhanced comments and descriptions in meta.yml files for better understanding of input and output structures. - Adjusted test cases in fastq_align_dedup workflows to reflect changes in input structure from single-end to paired-end. - Updated version numbers in test snapshots to reflect recent changes. * fix: pre-commit lint fixes * Update test files for Glimpse (#9467) * Update glimpse * Update chunk * Update concordance * Revert changes * Fix glimpse test * Fix glimpse * Fix glimpse2 tests * Update sbwf * Remove old snapshots * Update glimpse * Update modules/nf-core/glimpse2/concordance/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update test --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * meta.yml schema: add `containers` section, fix order and simplify (#9503) * fix order * add container section * simplify schema * require https for singluarity * update and add topics to snakemake module (#9454) * update and add topics * add new topics structure * add stub test and capture version in snapshot * update to 9.14.0 * fix singularity be setting cache_dir * fix stub --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> * fix sambamba depth stub version (#9509) * fix stub version * stray module * anota2seq: wrong variable name for batch assignment (#9511) rename variable * fix(anota2seq): add gene IDs and handle empty results (#9510) - Add missing gene_id_col parameter definition (defaults to 'gene_id') - Include gene IDs as first column in all results tables using configurable column name - Only write output files when there are significant results to avoid empty files - Mark all results TSV outputs as optional since they're conditionally created - Update test to use buffering results instead of empty mRNA_abundance results - Update test snapshots with new file formats including gene_id column This ensures anota2seq results are consistent with other modules and include gene identifiers for downstream analysis, while gracefully handling cases where no genes pass significance thresholds. Co-authored-by: Sebastian Uhrig <[email protected]> * fix(decoupler): reorder imports and ensure environment variables are … (#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules * Add strdrop/build (#9512) Add strdrop build * chore(deps): update infrastructural dependencies * 🔧 update image and bioconda container for VueGen to latest version (#9201) * 🔧 update image and bioconda container to latest version * ✅ update test snapshots * 🐛 fix display of version of vuegen - had no command line interface option to display version, see Multiomics-Analytics-Group/vuegen#167 * 🎨 display versions.yml content in snapshots * 🔧 add Dockerfile to install lastet PyPI vuegen version - does not pass hadolint(er) as of now * 🚧 add wave containers * 🔥 remove README again * 🔥 remove Dockerfile again * 🚧 try to follow Mahesh's advice * 🐛 add explicit cache directory * 🔧 bump to Python 3.12 and remove channel prefix * 🔧 specify singularity image with https ... as specified in the docs: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers * 🚧 set user specified R libarary folder * ⏪ make docker and conda work again (using nf-core 3.5.1) * 🔧 switch again to custom docker image instead of wave - wave leads to too many custom installation issues * 🐛 try to add font package * 🔥 remove code moved to image - singularity runs in devcontainer * ⏪ add back conda quarto flag * 🎨 remove trailing whitespace * 🎨 format again * 🎨 hopefully the last trailing whitespace * 📝 document the build process and why the container is needed * Update image with nf-core one Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update container name Co-authored-by: Matthias Hörtenhuber <[email protected]> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * qsv/cat: bump version (#9518) Bump qsv * Update haplogrep3 recipe to use topics (#9523) Co-authored-by: nf-core-bot <[email protected]> * semibin/singleeasybin: bump version + migrate to topics (#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove unused folder * rename * trimmomatic revisit * cutadapt revisit * trimgalore revisit * bbduk revisit * fastp revisit * adapterremoval revisit * leehom checkpoint (#9534) * leehom checkpoint * debugged with transpose and proper collect on nf-test * leehom change order * remove ngmerge because cant deal with /1 /2 paired reads * paired end no merge test * New module: clusty (#9533) * new module clusty * patch links docs * fix prettier * remove non-mandatory input 'algorithm' * also patch stub input * Bump TRGT to 4.1.0 (#9514) * Bump TRGT to 4.1.0 * Switch to topics * Update modules/nf-core/trgt/genotype/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * fix missing quotes (#9535) * Fix dream to show more than 10 results (#9507) * fix: dream to show more than 10 results * test: update snapshots * test: update snapshots * feat: add round digits option and update snapshots again * fix: improve code formatting and update test snapshots * Fix tests and update snapshots * Update snapshot for `abundance_differential_filter` subworkflow * Fix tests with unstable content * Fix unstable files in test for `abundance_differential_filter` subworkflow --------- Co-authored-by: Anabella Trigila <[email protected]> * rename to more appropriate fastq_preprocess_seqkit (#9537) * New module - TD2 (added modules for td2.longorfs & td2.predict) (#9475) * added modules for td2.longorfs & td2.predict * changes to version handling, updated snaps, and tests - resolving comments * added topics section in meta.yml * fix topics section in meta.yml * Update modules/nf-core/td2/longorfs/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Update main.nf - stub run * Update meta.yml * resolving comments * updated emad ontologies * Update modules/nf-core/td2/predict/tests/main.nf.test.snap * Update modules/nf-core/td2/predict/main.nf * Update modules/nf-core/td2/longorfs/tests/main.nf.test.snap * Update modules/nf-core/td2/longorfs/main.nf * Update modules/nf-core/td2/predict/tests/main.nf.test.snap * Update modules/nf-core/td2/longorfs/tests/main.nf.test.snap --------- Co-authored-by: Simon Pearce <[email protected]> * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (#9531) * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(GavinHaLab/ichorCNA#26). It is unclear when a new version will be out, so I have patched the current bioconda package (bioconda/bioconda-recipes#61045) and built new container images, which I want to update to in this PR. * Update some md5sums * Update test snapshot * Update test snapshot * RSeQC split_bam.py module implementation (#9536) * RSeQC split_bam.py module implementation Syntax edit Refractored version channel to topic Cleanup * Update modules/nf-core/rseqc/splitbam/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Updated snapshot --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * remove topics from multiqc (#9530) * remove topics from multiqc * versions_multiqc -> versions * Apply suggestion from @nvnieuwk * fix meta.yml after merge * bump to MultiQC version 1.33 (#9538) * bump to 1.33 * update snapshots --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * Add strdrop/call (#9513) * Add strdrop build * Add strdrop/call * remove tag * fix wrong parameter name in error * align * remove duplicate versions * snaps * figure out why snapshots are not stable * different versions of trgt used in setup * Bump TRGT to 5.0.0 (#9541) 5.0.0 * Channel -> channel in some subwfs (#9542) Channel -> channel * Migrate cat/fastq to topic channel (#9543) * Migrate cat/fastq to topic channel * Remove out.versions in related subworkflows * Update snapshots (again) * Add module picard/collectvariantcallingmetrics (#9502) * Add module picard/collectvariantcallingmetrics * Run prettier * Fix format * Make one input tuple * Change test input structure * Add md5 checksum * Update snapshot * Update meta.yml * Support multithreading * Remove TODO Co-authored-by: Famke Bäuerle <[email protected]> --------- Co-authored-by: Famke Bäuerle <[email protected]> * fix tabix/tabix stub (#9544) * fix tabix stub * bump max shards to 16 * Unify msa modules (#9539) * add mafft_align subworkflow to prepare channels for mafft/align like all other msa modules * default output format fasta for tcoffee align and regressive to match other msa modules * [automated] Fix linting with Prettier * Update subworkflows/nf-core/mafft_align/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> --------- Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Fix missing version from subworkflow snapshot (#9548) * New module: whatshap/phase (#9431) * add whatshap phase module * change the vcf-specific test * change test * add versions * remove snapshot * update snapshot * Update modules/nf-core/whatshap/phase/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * rm unused args * add snapshot * add ontologies * update the snapshot * add versions to snapshot * fix stub issues * update the test and snap * fix format with "nextflow lint" * fix hardcoded name and file name ambiguity problem --------- Co-authored-by: Famke Bäuerle <[email protected]> * Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (#9549) * bump version cat/cat * reinclude cat tags for other modules * patch test name & meta.yml * Update main.nf.test * plastid metagene_generate, make_wiggle, psite (#9482) * plastid metagene_generate, make_wiggle, psite * pair BAM and BAI files * pair bam and p_offsets * omit optional arguments * metagene generate accepts various input formats * add meta * do not remove variable headers from output files * warning about hard-coded version * make lint happy * make lint happy #2 * plastid/make_wiggle: nf-core standards compliance - Add mapping_rule val input (enum: fiveprime, threeprime, center, fiveprime_variable) - Move output_format to ext.args (optional arg per nf-core standards) - Add validation: error if p_offsets missing with fiveprime_variable - Remove hardcoded --fiveprime_variable - Update meta.yml with mapping_rule input and enum - Update tests with mapping_rule input 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * adapt meta.yml to new parameters * plastid: consolidate test snapshots and fix reproducibility - Consolidate multiple snapshot assertions into single snapshots per test - Remove snapshots of empty stub files (just check existence) - Exclude non-reproducible PNG from psite snapshots (matplotlib drift) - Format metagene_generate command across multiple lines 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * plastid/make_wiggle: remove tracks from snapshot Wig files have non-reproducible md5sums across environments. Content is already validated via getText().contains('track'). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * plastid/psite: remove non-reproducible outputs from snapshot metagene_profiles.txt and p_offsets.txt have non-reproducible md5sums. Content is already validated via getText().contains() checks. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude Opus 4.5 <[email protected]> * Add index and threads to trgt/merge (#9545) * Fix test path modification (#9465) * Update bcftools * Update bcftools csq * Update somalier ancestry * Update bcftools pluginfilltags * Update cnvnator * Update snap cnvnator * Fix extract somalier sbwf * Update snapshot * Update md5 * Fix linting * Upd snapshot * Upd snapshot * Upd snapshot * Upd snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update xenium ranger modules and subworkflows (#9525) * update xeniumranger modules to use xeniumranger v4.0 * update xeniumranger modules to use xeniumranger v4.0 * fix: update xeniumranger import-segmentation tests and logic * update test compute resource spec to follow 10x website * remove extra file * fix: apply topic channels and update meta.yml structure for xeniumranger * fix: update meta.yml structure to satisfy schema * fix: align meta.yml with topic versions blog post example * fix: update meta.yml topics structure to satisfy schema validation * fix: automated lint fix for meta.yml topics structure * fix: use standard container definition syntax * fix: apply topic versions to rename module * fix: apply topic versions and meta.yml schema fixes for xeniumranger modules and subworkflows * untrack files * remove test config files for github workflow * remove config def in tests * remove config def in tests * Update tests and snapshots for xeniumranger modules and subworkflows * remove subworkflows for xeniumranger * remove subworkflows for xeniumranger * fix: update test template * fix relabel meta.yml * make prek hppy * make prek hppy * make prek hppy * update import-segmentation doc * update import-segmentation doc * fix oncologies * Fix snapshot file key order for rename and resegment modules * Apply suggestions from code review Co-authored-by: Copilot <[email protected]> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <[email protected]> Co-authored-by: Sameesh Kher <[email protected]> Co-authored-by: Copilot <[email protected]> * Version update: Modkit repair, callmods and bedmethyltobigwig (#9547) * update to v0.6 * update to v0.6 * update to v0.6 * update yml * update to v0.6 * update snapshot * update snapshot --------- Co-authored-by: ra25wog <[email protected]> * Update `GLIMPSE` sbwf (#9524) * Update glimpse sbwf * Update test * Update filter operation * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add quilt imputation subworkflow (#9443) * Add sbwf quilt * Fix tags * Update meta * Use modules repo files * Update glimpse2 imputation subworkflow (#9434) * Update glimpse2 sbwf * Update test * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf Co-authored-by: Jonathan Manning <[email protected]> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <[email protected]> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> * Add `BEAGLE5` imputation subworkflow (#9550) * Update glimpse2 sbwf * Update test * Add region to beagle5 * Add subworkflow * Fix linting * Fix linting * Fix linting * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add comment * Update grouping and test * Remove tag * Revert change glimpse2 reference * Revert change glimpse2 sbwf * Revert change glimpse2 sbwf * Revert change glimpse2 sbwf --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add minimac4 imputation subworkfllow (#9451) * Add vcf_impute_minimac4 * Update linting * Update test * Fix linting * Update minimac4 sbwf * Remove tag * Remove tag * Fix linting * Add comment * Update snapshot * Fix nf-test * Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow (#9559) Add BBSplit stats to MultiQC files in fastq_qc_trim_filter_setstrandedness Pass BBSplit stats output to MultiQC for visualization of read binning statistics. MultiQC 1.33+ includes support for parsing BBSplit stats.txt files and displaying per-sample read distribution across reference genomes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Update cutadapt (#9551) * proper stub for gz and stub test added * topic output syntax and tests update * meta yml updated with topics and ontologies * meta file curated * version bump to latest * update nf-tests properly * adding self to maintainers * removed Z flag as is deprecated after v4.10 * conda bug with different pre-built python version fixed * added cutadapt to stub now that stub gz is properly created, and removed cutadapt versions, since it is now ported to topics * single-end test with tool skips * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (#9553) * update yaml * update main.nf * modified test runs * update bedmethyltobigwig tests * update main * update snapshot * fix linting * update snapshots * remove config * update module_args * [automated] Fix linting with Prettier * changed name * update main --------- Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * latest container, with cutadapt 5.2 * new output syntax, nf-tests updated, meta updated * meta yml lint fixed * trying to fix lint * lint fix with nf-core tools 3.6.0dev * removing TRIMGALORE versions output from the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <[email protected]> * trimgalore output versions removed * structure for subworkflow outputs in meta.yml file * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * main and meta updated with new one-tool logic * nf-tests updated * var name change * paired_interleaved dropped * adapterremoval merge logic update similar to eager * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: Hanh Hoang <[email protected]> Co-authored-by: Delfina Terradas <[email protected]> Co-authored-by: Peter Pruisscher <[email protected]> Co-authored-by: Ramprasad Neethiraj <[email protected]> Co-authored-by: Matthias De Smet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude <[email protected]> Co-authored-by: Diego Alvarez S. <[email protected]> Co-authored-by: Nathan Weeks <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Sebastian Uhrig <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: vagkaratzas <[email protected]> Co-authored-by: Evangelos Karatzas <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Sameesh Kher <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Luca Beltrame <[email protected]> Co-authored-by: Rayan Hassaïne <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: Adrien Coulier <[email protected]> Co-authored-by: Georgia Kesisoglou <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> Co-authored-by: HD Yi <[email protected]> Co-authored-by: Dongze He <[email protected]> Co-authored-by: Dongze He <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]>

@mashehu

…9521) * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests * Add ontologies to tcoffee/regressive and upp/align modules (#9484) * add ontologies to tcoffee regressive * add ontologies to upp align * Add module PBMARKDUP (#9457) * Add module pbmarkdup * Fix linting * Update path to test data * Update with code review (--dup-file, log, check file name collisions) * Fix linting * Update path to test data * Update modules/nf-core/pbmarkdup/meta.yml * Fix linting * Enable complex contrast strings in DESeq2 (#9473) * Enable complex contrast strings * Update docker image * Add test case with limma contrast string * Format changes and add test with shrinkage * Declare deepvariant optional html output (#9469) * Add deepvariant optional html * update snapshot * Update modules/nf-core/deepvariant/rundeepvariant/main.nf Co-authored-by: Ramprasad Neethiraj <[email protected]> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <[email protected]> * utils_nfcore_pipeline: fix small lang server error (#9492) fix small lang server error * Fix hisat2/align to support large genome indices (.ht2l) (#9493) HISAT2 uses .ht2l extension instead of .ht2 for large genomes. Updated index detection to match both extensions. Related to nf-core/rnaseq#1643 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude <[email protected]> * Update shinyngs modules to latest release (#9488) * Update semibin/singleeasybin environment (#9495) * add new ontology term to tcoffee align (#9497) * tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (#9489) * Sort file listing so "first" file is deterministic * Declare closure parameter per strict syntax Co-authored-by: Matthias Hörtenhuber <[email protected]> --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> * Sambamba depth add region bed input (#9498) * sambamba add region bed input * fix linting * fix linting * Apply suggestions from code review Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * fix fasta_index_methylseq and fastq_align_dedup workflows (#9496) * fix fasta_index_methylseq and fastq_align_dedup workflows for clarity and consistency - Updated variable names in fasta_index_methylseq to use 'channel' instead of 'Channel' for consistency. - Renamed UNTAR to UNTAR_BISMARK and UNTAR_BWAMETH for clarity in fasta_index_methylseq. - Enhanced comments and descriptions in meta.yml files for better understanding of input and output structures. - Adjusted test cases in fastq_align_dedup workflows to reflect changes in input structure from single-end to paired-end. - Updated version numbers in test snapshots to reflect recent changes. * fix: pre-commit lint fixes * Update test files for Glimpse (#9467) * Update glimpse * Update chunk * Update concordance * Revert changes * Fix glimpse test * Fix glimpse * Fix glimpse2 tests * Update sbwf * Remove old snapshots * Update glimpse * Update modules/nf-core/glimpse2/concordance/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update test --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * meta.yml schema: add `containers` section, fix order and simplify (#9503) * fix order * add container section * simplify schema * require https for singluarity * update and add topics to snakemake module (#9454) * update and add topics * add new topics structure * add stub test and capture version in snapshot * update to 9.14.0 * fix singularity be setting cache_dir * fix stub --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> * fix sambamba depth stub version (#9509) * fix stub version * stray module * anota2seq: wrong variable name for batch assignment (#9511) rename variable * fix(anota2seq): add gene IDs and handle empty results (#9510) - Add missing gene_id_col parameter definition (defaults to 'gene_id') - Include gene IDs as first column in all results tables using configurable column name - Only write output files when there are significant results to avoid empty files - Mark all results TSV outputs as optional since they're conditionally created - Update test to use buffering results instead of empty mRNA_abundance results - Update test snapshots with new file formats including gene_id column This ensures anota2seq results are consistent with other modules and include gene identifiers for downstream analysis, while gracefully handling cases where no genes pass significance thresholds. Co-authored-by: Sebastian Uhrig <[email protected]> * fix(decoupler): reorder imports and ensure environment variables are … (#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules * Add strdrop/build (#9512) Add strdrop build * chore(deps): update infrastructural dependencies * 🔧 update image and bioconda container for VueGen to latest version (#9201) * 🔧 update image and bioconda container to latest version * ✅ update test snapshots * 🐛 fix display of version of vuegen - had no command line interface option to display version, see Multiomics-Analytics-Group/vuegen#167 * 🎨 display versions.yml content in snapshots * 🔧 add Dockerfile to install lastet PyPI vuegen version - does not pass hadolint(er) as of now * 🚧 add wave containers * 🔥 remove README again * 🔥 remove Dockerfile again * 🚧 try to follow Mahesh's advice * 🐛 add explicit cache directory * 🔧 bump to Python 3.12 and remove channel prefix * 🔧 specify singularity image with https ... as specified in the docs: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers * 🚧 set user specified R libarary folder * ⏪ make docker and conda work again (using nf-core 3.5.1) * 🔧 switch again to custom docker image instead of wave - wave leads to too many custom installation issues * 🐛 try to add font package * 🔥 remove code moved to image - singularity runs in devcontainer * ⏪ add back conda quarto flag * 🎨 remove trailing whitespace * 🎨 format again * 🎨 hopefully the last trailing whitespace * 📝 document the build process and why the container is needed * Update image with nf-core one Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update container name Co-authored-by: Matthias Hörtenhuber <[email protected]> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * qsv/cat: bump version (#9518) Bump qsv * Update haplogrep3 recipe to use topics (#9523) Co-authored-by: nf-core-bot <[email protected]> * semibin/singleeasybin: bump version + migrate to topics (#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove unused folder * rename * trimmomatic revisit * cutadapt revisit * trimgalore revisit * bbduk revisit * fastp revisit * adapterremoval revisit * leehom checkpoint (#9534) * leehom checkpoint * debugged with transpose and proper collect on nf-test * leehom change order * remove ngmerge because cant deal with /1 /2 paired reads * paired end no merge test * New module: clusty (#9533) * new module clusty * patch links docs * fix prettier * remove non-mandatory input 'algorithm' * also patch stub input * Bump TRGT to 4.1.0 (#9514) * Bump TRGT to 4.1.0 * Switch to topics * Update modules/nf-core/trgt/genotype/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * fix missing quotes (#9535) * Fix dream to show more than 10 results (#9507) * fix: dream to show more than 10 results * test: update snapshots * test: update snapshots * feat: add round digits option and update snapshots again * fix: improve code formatting and update test snapshots * Fix tests and update snapshots * Update snapshot for `abundance_differential_filter` subworkflow * Fix tests with unstable content * Fix unstable files in test for `abundance_differential_filter` subworkflow --------- Co-authored-by: Anabella Trigila <[email protected]> * rename to more appropriate fastq_preprocess_seqkit (#9537) * New module - TD2 (added modules for td2.longorfs & td2.predict) (#9475) * added modules for td2.longorfs & td2.predict * changes to version handling, updated snaps, and tests - resolving comments * added topics section in meta.yml * fix topics section in meta.yml * Update modules/nf-core/td2/longorfs/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Update main.nf - stub run * Update meta.yml * resolving comments * updated emad ontologies * Update modules/nf-core/td2/predict/tests/main.nf.test.snap * Update modules/nf-core/td2/predict/main.nf * Update modules/nf-core/td2/longorfs/tests/main.nf.test.snap * Update modules/nf-core/td2/longorfs/main.nf * Update modules/nf-core/td2/predict/tests/main.nf.test.snap * Update modules/nf-core/td2/longorfs/tests/main.nf.test.snap --------- Co-authored-by: Simon Pearce <[email protected]> * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (#9531) * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(GavinHaLab/ichorCNA#26). It is unclear when a new version will be out, so I have patched the current bioconda package (bioconda/bioconda-recipes#61045) and built new container images, which I want to update to in this PR. * Update some md5sums * Update test snapshot * Update test snapshot * RSeQC split_bam.py module implementation (#9536) * RSeQC split_bam.py module implementation Syntax edit Refractored version channel to topic Cleanup * Update modules/nf-core/rseqc/splitbam/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Updated snapshot --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * remove topics from multiqc (#9530) * remove topics from multiqc * versions_multiqc -> versions * Apply suggestion from @nvnieuwk * fix meta.yml after merge * bump to MultiQC version 1.33 (#9538) * bump to 1.33 * update snapshots --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * Add strdrop/call (#9513) * Add strdrop build * Add strdrop/call * remove tag * fix wrong parameter name in error * align * remove duplicate versions * snaps * figure out why snapshots are not stable * different versions of trgt used in setup * Bump TRGT to 5.0.0 (#9541) 5.0.0 * Channel -> channel in some subwfs (#9542) Channel -> channel * Migrate cat/fastq to topic channel (#9543) * Migrate cat/fastq to topic channel * Remove out.versions in related subworkflows * Update snapshots (again) * Add module picard/collectvariantcallingmetrics (#9502) * Add module picard/collectvariantcallingmetrics * Run prettier * Fix format * Make one input tuple * Change test input structure * Add md5 checksum * Update snapshot * Update meta.yml * Support multithreading * Remove TODO Co-authored-by: Famke Bäuerle <[email protected]> --------- Co-authored-by: Famke Bäuerle <[email protected]> * fix tabix/tabix stub (#9544) * fix tabix stub * bump max shards to 16 * Unify msa modules (#9539) * add mafft_align subworkflow to prepare channels for mafft/align like all other msa modules * default output format fasta for tcoffee align and regressive to match other msa modules * [automated] Fix linting with Prettier * Update subworkflows/nf-core/mafft_align/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> --------- Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Fix missing version from subworkflow snapshot (#9548) * New module: whatshap/phase (#9431) * add whatshap phase module * change the vcf-specific test * change test * add versions * remove snapshot * update snapshot * Update modules/nf-core/whatshap/phase/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * rm unused args * add snapshot * add ontologies * update the snapshot * add versions to snapshot * fix stub issues * update the test and snap * fix format with "nextflow lint" * fix hardcoded name and file name ambiguity problem --------- Co-authored-by: Famke Bäuerle <[email protected]> * Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (#9549) * bump version cat/cat * reinclude cat tags for other modules * patch test name & meta.yml * Update main.nf.test * plastid metagene_generate, make_wiggle, psite (#9482) * plastid metagene_generate, make_wiggle, psite * pair BAM and BAI files * pair bam and p_offsets * omit optional arguments * metagene generate accepts various input formats * add meta * do not remove variable headers from output files * warning about hard-coded version * make lint happy * make lint happy #2 * plastid/make_wiggle: nf-core standards compliance - Add mapping_rule val input (enum: fiveprime, threeprime, center, fiveprime_variable) - Move output_format to ext.args (optional arg per nf-core standards) - Add validation: error if p_offsets missing with fiveprime_variable - Remove hardcoded --fiveprime_variable - Update meta.yml with mapping_rule input and enum - Update tests with mapping_rule input 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * adapt meta.yml to new parameters * plastid: consolidate test snapshots and fix reproducibility - Consolidate multiple snapshot assertions into single snapshots per test - Remove snapshots of empty stub files (just check existence) - Exclude non-reproducible PNG from psite snapshots (matplotlib drift) - Format metagene_generate command across multiple lines 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * plastid/make_wiggle: remove tracks from snapshot Wig files have non-reproducible md5sums across environments. Content is already validated via getText().contains('track'). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * plastid/psite: remove non-reproducible outputs from snapshot metagene_profiles.txt and p_offsets.txt have non-reproducible md5sums. Content is already validated via getText().contains() checks. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude Opus 4.5 <[email protected]> * Add index and threads to trgt/merge (#9545) * Fix test path modification (#9465) * Update bcftools * Update bcftools csq * Update somalier ancestry * Update bcftools pluginfilltags * Update cnvnator * Update snap cnvnator * Fix extract somalier sbwf * Update snapshot * Update md5 * Fix linting * Upd snapshot * Upd snapshot * Upd snapshot * Upd snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update xenium ranger modules and subworkflows (#9525) * update xeniumranger modules to use xeniumranger v4.0 * update xeniumranger modules to use xeniumranger v4.0 * fix: update xeniumranger import-segmentation tests and logic * update test compute resource spec to follow 10x website * remove extra file * fix: apply topic channels and update meta.yml structure for xeniumranger * fix: update meta.yml structure to satisfy schema * fix: align meta.yml with topic versions blog post example * fix: update meta.yml topics structure to satisfy schema validation * fix: automated lint fix for meta.yml topics structure * fix: use standard container definition syntax * fix: apply topic versions to rename module * fix: apply topic versions and meta.yml schema fixes for xeniumranger modules and subworkflows * untrack files * remove test config files for github workflow * remove config def in tests * remove config def in tests * Update tests and snapshots for xeniumranger modules and subworkflows * remove subworkflows for xeniumranger * remove subworkflows for xeniumranger * fix: update test template * fix relabel meta.yml * make prek hppy * make prek hppy * make prek hppy * update import-segmentation doc * update import-segmentation doc * fix oncologies * Fix snapshot file key order for rename and resegment modules * Apply suggestions from code review Co-authored-by: Copilot <[email protected]> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <[email protected]> Co-authored-by: Sameesh Kher <[email protected]> Co-authored-by: Copilot <[email protected]> * Version update: Modkit repair, callmods and bedmethyltobigwig (#9547) * update to v0.6 * update to v0.6 * update to v0.6 * update yml * update to v0.6 * update snapshot * update snapshot --------- Co-authored-by: ra25wog <[email protected]> * Update `GLIMPSE` sbwf (#9524) * Update glimpse sbwf * Update test * Update filter operation * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add quilt imputation subworkflow (#9443) * Add sbwf quilt * Fix tags * Update meta * Use modules repo files * Update glimpse2 imputation subworkflow (#9434) * Update glimpse2 sbwf * Update test * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf Co-authored-by: Jonathan Manning <[email protected]> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <[email protected]> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> * Add `BEAGLE5` imputation subworkflow (#9550) * Update glimpse2 sbwf * Update test * Add region to beagle5 * Add subworkflow * Fix linting * Fix linting * Fix linting * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add comment * Update grouping and test * Remove tag * Revert change glimpse2 reference * Revert change glimpse2 sbwf * Revert change glimpse2 sbwf * Revert change glimpse2 sbwf --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add minimac4 imputation subworkfllow (#9451) * Add vcf_impute_minimac4 * Update linting * Update test * Fix linting * Update minimac4 sbwf * Remove tag * Remove tag * Fix linting * Add comment * Update snapshot * Fix nf-test * Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow (#9559) Add BBSplit stats to MultiQC files in fastq_qc_trim_filter_setstrandedness Pass BBSplit stats output to MultiQC for visualization of read binning statistics. MultiQC 1.33+ includes support for parsing BBSplit stats.txt files and displaying per-sample read distribution across reference genomes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Update cutadapt (#9551) * proper stub for gz and stub test added * topic output syntax and tests update * meta yml updated with topics and ontologies * meta file curated * version bump to latest * update nf-tests properly * adding self to maintainers * removed Z flag as is deprecated after v4.10 * conda bug with different pre-built python version fixed * added cutadapt to stub now that stub gz is properly created, and removed cutadapt versions, since it is now ported to topics * single-end test with tool skips * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (#9553) * update yaml * update main.nf * modified test runs * update bedmethyltobigwig tests * update main * update snapshot * fix linting * update snapshots * remove config * update module_args * [automated] Fix linting with Prettier * changed name * update main --------- Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * latest container, with cutadapt 5.2 * new output syntax, nf-tests updated, meta updated * meta yml lint fixed * trying to fix lint * lint fix with nf-core tools 3.6.0dev * removing TRIMGALORE versions output from the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <[email protected]> * trimgalore output versions removed * structure for subworkflow outputs in meta.yml file * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * main and meta updated with new one-tool logic * nf-tests updated * var name change * paired_interleaved dropped * adapterremoval merge logic update similar to eager * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: Hanh Hoang <[email protected]> Co-authored-by: Delfina Terradas <[email protected]> Co-authored-by: Peter Pruisscher <[email protected]> Co-authored-by: Ramprasad Neethiraj <[email protected]> Co-authored-by: Matthias De Smet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude <[email protected]> Co-authored-by: Diego Alvarez S. <[email protected]> Co-authored-by: Nathan Weeks <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Sebastian Uhrig <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: vagkaratzas <[email protected]> Co-authored-by: Evangelos Karatzas <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Sameesh Kher <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Luca Beltrame <[email protected]> Co-authored-by: Rayan Hassaïne <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: Adrien Coulier <[email protected]> Co-authored-by: Georgia Kesisoglou <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> Co-authored-by: HD Yi <[email protected]> Co-authored-by: Dongze He <[email protected]> Co-authored-by: Dongze He <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]>

* Add fq2bam fq align dd bwamem (#9309) * Added fq2bam * test fix * typo * PE channel * tidying * gpu snap * test fix for snaps * gpu snapshot * PR feedback * tests * cpu snapshot * tests * last snapshot * fix channels * last snapshot * PR feedback * PR feedback * new cpu snapshot * changing test * changing test * new gpu snapshot * [automated] Update gpu snapshot * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * containerOptions back * genome test name * genome test name * wrong comment * fix tests * new snapshot * Add use_gpu channel * new snapshot * [automated] Fix linting with Prettier * fix lint * Remove containerOptions --------- Co-authored-by: root <[email protected]> Co-authored-by: root <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Eduard Casas <[email protected]> * Update RSEQC modules with Seqera Wave containers matching environment.yml (#9588) Replace biocontainers with Seqera Wave containers built from the exact environment.yml specifications. This ensures conda and container environments match. Key changes: - Pin r-base=4.3 in all RSEQC environment.yml files (r-base=3.5 has no ARM build available) - Use Wave-generated containers built from environment.yml for both Docker and Singularity - Standardize all 9 RSEQC modules to use identical dependencies The previous biocontainers (rseqc:5.0.4--pyhdfd78af_1) were not built with the R pin specified in environment.yml, causing inconsistency between conda and container execution modes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Allow gzipped inputs to modkit/bedmethyltobigwig (#9591) * Allow gzipped inputs to modkit/bedmethyltobigwig * Update modules/nf-core/modkit/bedmethyltobigwig/main.nf Co-authored-by: Felix Kummer <[email protected]> * harshil --------- Co-authored-by: Felix Kummer <[email protected]> * Fix modkit pileup stub (#9590) * feat(ribowaltz): Export underlying data from QC plots (#9593) * feat(ribowaltz): Export underlying data from QC plots Add TSV export for data underlying P-site region and frame distribution plots. This makes the raw data available for downstream analysis and reporting tools like MultiQC. Changes: - Export psite_region.tsv from region_psite() in save_psite_region_plot - Export frames.tsv from frame_psite() in save_frame_plots - Export frames_stratified.tsv from frame_psite_length() in save_frame_plots - Add ribowaltz_qc_data output channel for TSV files - Update stub outputs to include new TSV files - Add test assertions for new output channel 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * chore(ribowaltz): Update meta.yml with ribowaltz_qc_data output 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Claude Opus 4.5 <[email protected]> * feat(ribowaltz): Export underlying data for all QC plots (#9594) * feat(ribowaltz): Export underlying data for all QC plots Add TSV data exports for all riboWaltz QC plots to enable downstream processing and MultiQC custom content integration: - length_bins_for_psite.tsv (P-site offset identification bins) - ends_heatmap.tsv (read extremities heatmap) - codon_usage.tsv (codon usage barplot) - length_distribution.tsv (read length distribution) - metaprofile_psite.tsv (P-site metaprofile around start/stop codons) These complement existing exports (psite_region, frames, frames_stratified). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * fix(ribowaltz): Use correct key for ends_heatmap data export The rends_heat function returns data in 'count_dt' not 'dt'. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Claude Opus 4.5 <[email protected]> * chore(deps): update conda-incubator/setup-miniconda digest to 8352349 * Swap bcftools/mpileup to topic (#9596) * Swap bcftools/mpileup to topic * Fix linting * Update snapshots * Swap mpileup to topics (#9595) * Swap mpileup to topics * Apply suggestions from code review * Add Harshil back as author * Update snapshots * Fix string path (#9602) * Fix string path * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * Bump genmod to 3.10.2 and switch to topics (#9603) * Bump genmod to 3.10.2 and switch to topics * Add md5sum for stable subcommands * Update the FASTP output file names to match "R1/R2" naming conventions (#9606) * Modify output files in FASTP module to use 'R1' and 'R2' conventions rather than just '1' or '2' * Update testing snapshots --------- Co-authored-by: Tatiana Gelaf Romer <[email protected]> * Update MLST from 2.23 to 2.25 (#9604) * Update MLST from 2.23 to 2.25 * test: update snapshots for mlst 2.25 --------- Co-authored-by: Subham Verma <[email protected]> * Update GitHub PR template check list item - version numbers (#9586) Update PR template check list item WRT version numbers Updating the PR template per the blog: ``` We are adopting topic channels to replace the versions.yml. For now both options are valid, but this will change. No more mixing of version channels. ``` Co-authored-by: Simon Pearce <[email protected]> * Ngscheckmate topics (#9597) * Start of topics conversion * Swap ngscheckmate to topic * Remove trailing whitespace * Update snapshots * Update test * Update snapshots * Skip two submodules on conda * Address comments * Update snapshot * Update snapshot --------- Co-authored-by: Louis Le Nézet <[email protected]> * Migrate samtools dict/faidx/merge to topics (#9598) * Update samtools dict/faidx/merge * Update subworkflows * Update meta * Update snapshots * Prettier * Add config back * Add config * Prettier * Allow `dream` to process non-formula contrasts (#9562) * Allow `dream` to process non-formula contrasts * Add test case without formula * Update `meta.yml` * Fix test with unstable file * Update subworkflow to allow non-formula contrasts with DREAM * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <[email protected]> * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <[email protected]> * Correct format of function * Fix contrast building and code flow * Update tests * Modify logic for contrast_string building * Make contrast_string compulsory with formula * Update tests * Refactor contrast_string construction logic Simplified the construction of contrast_string by removing unnecessary checks for treatment levels in the design matrix. * Make formula mutually exclusive to contrast tuple * Modify tests with mutually exclusive varaibles * Revert changes in first test case * Update tests * Fix tests --------- Co-authored-by: Copilot <[email protected]> * Add vcfpgloader/load module (#9579) * Add vcfpgloader/load module High-throughput VCF to PostgreSQL loader using asyncpg for bulk variant ingestion. * Remove throughput metric from meta.yml description * fix(vcfpgloader): fix CI failures for conda, singularity, and docker - Add pip as explicit conda dependency in environment.yml - Simplify container directive (remove oras:// for singularity compatibility) - Remove integration test requiring PostgreSQL database 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * chore: re-trigger CI for bioconda 0.5.3 propagation * chore: reorder deps to bust conda cache for 0.5.3 * fix: specify exact bioconda build string to force 0.5.3 * chore: sort environment.yml dependencies (linter) * fix: remove version from snapshot (varies by profile) * fix(vcfpgloader): restore version checking in tests Add back versions to snapshot assertions and update snapshot file with expected version output format for lint compliance. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * fix(vcfpgloader): use correct findAll pattern for topic versions Use process.out.findAll { key, val -> key.startsWith("versions")} pattern for topic-based versioning, matching nf-core conventions. Update snapshot with versions_vcfpgloader object format. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * feat(vcfpgloader): bump to v0.5.4 - Update environment.yml to bioconda::vcf-pg-loader=0.5.4 - Update container to ghcr.io/zacharyr41/vcf-pg-loader:0.5.4 - Add sed to parse version number from --version output - Update snapshot for 0.5.4 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * ci: retrigger after bioconda 0.5.4 merge * fix(vcfpgloader): update meta.yml version format Add type: eval and description to version command entries in outputs and topics sections. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * style(vcfpgloader): apply nextflow lint formatting * fix(vcfpgloader): add export to env() output variables Add explicit `export` to ROWS_LOADED assignments as recommended for env() output qualifiers. Note: `nextflow lint` still reports false positive errors for env() outputs - this is a known limitation of static analysis on shell scripts. The linter cannot verify variable definitions inside heredoc script blocks. Other nf-core modules (e.g., genescopefk) have the same lint warning. The code functions correctly at runtime. * Update modules/nf-core/vcfpgloader/load/tests/nextflow.config Co-authored-by: Famke Bäuerle <[email protected]> * chore(vcfpgloader): remove unused tags.yml * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * refactor(vcfpgloader): consolidate inputs into single tuple * feat(vcfpgloader): switch to BioContainers - Use BioContainers URLs instead of personal ghcr.io - Remove jq dependency, use Python for JSON parsing - Fix sed quoting for nf-core lint compatibility 🤖 Generated with [Claude Code](https://claude.ai/code) * fix(vcfpgloader): update snapshots to include row_count output Add missing row_count and log outputs to test snapshots to match the process outputs being asserted in tests. --------- Co-authored-by: Claude <[email protected]> Co-authored-by: Zachary Rothstein <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * Replace busybox with coreutils sort for genmod modules (#9610) Replace busybox with coreutils sort * Hiphase: bump to version 1.5.0; use wave container; emit phased bam file (#9477) * update hiphase verstion to 1.5.0 * add the *.phased.bam as an output file * update test snapshot * change label to process_medium * improved the format * Sawfish discover: allow `genome.gclevels.mpack` emission to be optional (#9609) * allow genome.gclevels.mpack emission optional * update snapshot * edit snaptest to check if process.out.candidate_sv_bcf.csi exists, not the file size. * Update modules/nf-core/sawfish/discover/tests/main.nf.test to test check the name of `candidate_sv_bcf_csi` instead of file existence. Co-authored-by: Simon Pearce <[email protected]> * remove checking `candidate.sv.bcf.csi` file existence --------- Co-authored-by: Simon Pearce <[email protected]> * Add module t1k/run (#9555) * Initial commit * Create one input tuple * Remove bam tests * Update snapshot * Fix formatting * Update meta.yml * Add version to main.nf.test * Run prettier * Add minimac4 imputation subworkfllow (#9451) * Add vcf_impute_minimac4 * Update linting * Update test * Fix linting * Update minimac4 sbwf * Remove tag * Remove tag * Fix linting * Add comment * Update snapshot * Fix nf-test * Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow (#9559) Add BBSplit stats to MultiQC files in fastq_qc_trim_filter_setstrandedness Pass BBSplit stats output to MultiQC for visualization of read binning statistics. MultiQC 1.33+ includes support for parsing BBSplit stats.txt files and displaying per-sample read distribution across reference genomes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Update cutadapt (#9551) * proper stub for gz and stub test added * topic output syntax and tests update * meta yml updated with topics and ontologies * meta file curated * version bump to latest * update nf-tests properly * adding self to maintainers * removed Z flag as is deprecated after v4.10 * conda bug with different pre-built python version fixed * Syntax updates and topic version for manta modules (#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (#9553) * update yaml * update main.nf * modified test runs * update bedmethyltobigwig tests * update main * update snapshot * fix linting * update snapshots * remove config * update module_args * [automated] Fix linting with Prettier * changed name * update main --------- Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (#9553) * update yaml * update main.nf * modified test runs * update bedmethyltobigwig tests * update main * update snapshot * fix linting * update snapshots * remove config * update module_args * [automated] Fix linting with Prettier * changed name * update main --------- Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * latest container, with cutadapt 5.2 * new output syntax, nf-tests updated, meta updated * meta yml lint fixed * trying to fix lint * lint fix with nf-core tools 3.6.0dev * removing TRIMGALORE versions output from the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <[email protected]> * RiboCode - prepare_transcripts, metaplots, ribocode (#9485) * add 3 required ribocode modules * GTFUpdate; meta in inputs; No Gzip; * return snaps * nf-test passing * Update RiboCode versions to use topics * Update RiboCode versions to use topics -New lines at EOF * Update RiboCode versions to use topics - Prettier * RiboCode update snapshots * Update RiboCode snapshots to container versions * Bump to latest ribocode build with pyfasta and ribocode fixes * Improve RiboCode module tests and fix review issues - Remove defaults channel from environment.yml files - Fix keywords to lowercase in meta.yml files - Add stub tests to all modules - Update version snapshots from 1.2.14 to 1.2.15 - Remove duplicate snapshot entries - Optimize test setup using pre-made test data: - metaplots/ribocode: use UNTAR for annotation instead of full setup chain - prepare: use pre-made updated GTF instead of running gtfupdate Temporarily points to test-datasets branch pending merge of: https://github.com/nf-core/test-datasets/pull/1820 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * Update RiboCode snapshot to GHA runner architecture Update md5 hashes to match linux/amd64 output from CI runners. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * Add schema reference to ribocode/ribocode meta.yml 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * Revert nf-test.config to standard test-datasets paths test-datasets PR #1820 has been merged, reverting to nf-core/test-datasets. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude Opus 4.5 <[email protected]> * Bump stranger (#9571) * Bump stranger * meta.yaml * linting not happy * linting is happy, but I'm not * pin same python version as used in container * add containers in meta.yml for fastqc and multiqc (#9569) * add containers for fastqc and multiqc * sort containers and add https for singularity * fix build_id naming * some more key names fixing * use underscores * Sort TRGT merge inputs for stable outputs (#9572) * Rseqc add bam index - topics-based versions - version bump (#9546) * Updated rseqc/bamstat: Added BAI support per #9460 & topics-based versions * Updated rseqc/inferexperiment: Added BAI support per #9460 & topics-based versions * Updated rseqc/innerdistance: Added BAI support per #9460 & topics-based versions * Updated rseqc/junctionannotation: Added BAI support per #9460 & topics-based versions * Updated rseqc/junctionsaturation: Added BAI support per #9460 & topics-based versions * Updated rseqc/readdistribution: Added BAI support per #9460 & topics-based versions * Updated rseqc/readduplication: Added BAI support per #9460 & topics-based versions * Updated rseqc/tin: Added topics-based versions * Updated bam_rseqc subworkflow - BAI support, channel syntax fix - topics-based versions * Failed snapshot update - linting error * Snapshot Update & Channel syntax fix * Channel syntax update * Test & Snapshot Updated - version assertion to circumvent nf-core tools potential bug * Fixed null entries in snapshot * Updated subworkflow assertions on optional files (& snapshot) - migration of versions channels to topics * Linting failures fixes - dedicated versions assertions * Add MultiQC routing for seqkit/stats and UMI-tools outputs (#9576) - Add SEQKIT_STATS output to multiqc_files in fastq_remove_rrna (when using ribodetector for rRNA removal) - Add umi_log output to multiqc_files in fastq_qc_trim_filter_setstrandedness for both trimgalore and fastp paths 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Update cmaple (#9580) * adding uncompression functionality * new versions output syntax * meta.yml updated * Add fq2bam fq align dd bwamem (#9309) * Added fq2bam * test fix * typo * PE channel * tidying * gpu snap * test fix for snaps * gpu snapshot * PR feedback * tests * cpu snapshot * tests * last snapshot * fix channels * last snapshot * PR feedback * PR feedback * new cpu snapshot * changing test * changing test * new gpu snapshot * [automated] Update gpu snapshot * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * PR feedback * containerOptions back * genome test name * genome test name * wrong comment * fix tests * new snapshot * Add use_gpu channel * new snapshot * [automated] Fix linting with Prettier * fix lint * Remove containerOptions --------- Co-authored-by: root <[email protected]> Co-authored-by: root <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Eduard Casas <[email protected]> * Update RSEQC modules with Seqera Wave containers matching environment.yml (#9588) Replace biocontainers with Seqera Wave containers built from the exact environment.yml specifications. This ensures conda and container environments match. Key changes: - Pin r-base=4.3 in all RSEQC environment.yml files (r-base=3.5 has no ARM build available) - Use Wave-generated containers built from environment.yml for both Docker and Singularity - Standardize all 9 RSEQC modules to use identical dependencies The previous biocontainers (rseqc:5.0.4--pyhdfd78af_1) were not built with the R pin specified in environment.yml, causing inconsistency between conda and container execution modes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Allow gzipped inputs to modkit/bedmethyltobigwig (#9591) * Allow gzipped inputs to modkit/bedmethyltobigwig * Update modules/nf-core/modkit/bedmethyltobigwig/main.nf Co-authored-by: Felix Kummer <[email protected]> * harshil --------- Co-authored-by: Felix Kummer <[email protected]> * Fix modkit pileup stub (#9590) * feat(ribowaltz): Export underlying data from QC plots (#9593) * feat(ribowaltz): Export underlying data from QC plots Add TSV export for data underlying P-site region and frame distribution plots. This makes the raw data available for downstream analysis and reporting tools like MultiQC. Changes: - Export psite_region.tsv from region_psite() in save_psite_region_plot - Export frames.tsv from frame_psite() in save_frame_plots - Export frames_stratified.tsv from frame_psite_length() in save_frame_plots - Add ribowaltz_qc_data output channel for TSV files - Update stub outputs to include new TSV files - Add test assertions for new output channel 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * chore(ribowaltz): Update meta.yml with ribowaltz_qc_data output 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Claude Opus 4.5 <[email protected]> * feat(ribowaltz): Export underlying data for all QC plots (#9594) * feat(ribowaltz): Export underlying data for all QC plots Add TSV data exports for all riboWaltz QC plots to enable downstream processing and MultiQC custom content integration: - length_bins_for_psite.tsv (P-site offset identification bins) - ends_heatmap.tsv (read extremities heatmap) - codon_usage.tsv (codon usage barplot) - length_distribution.tsv (read length distribution) - metaprofile_psite.tsv (P-site metaprofile around start/stop codons) These complement existing exports (psite_region, frames, frames_stratified). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * fix(ribowaltz): Use correct key for ends_heatmap data export The rends_heat function returns data in 'count_dt' not 'dt'. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Claude Opus 4.5 <[email protected]> * chore(deps): update conda-incubator/setup-miniconda digest to 8352349 * Swap bcftools/mpileup to topic (#9596) * Swap bcftools/mpileup to topic * Fix linting * Update snapshots * Swap mpileup to topics (#9595) * Swap mpileup to topics * Apply suggestions from code review * Add Harshil back as author * Update snapshots * Fix string path (#9602) * Fix string path * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * Bump genmod to 3.10.2 and switch to topics (#9603) * Bump genmod to 3.10.2 and switch to topics * Add md5sum for stable subcommands * Update the FASTP output file names to match "R1/R2" naming conventions (#9606) * Modify output files in FASTP module to use 'R1' and 'R2' conventions rather than just '1' or '2' * Update testing snapshots --------- Co-authored-by: Tatiana Gelaf Romer <[email protected]> * Update MLST from 2.23 to 2.25 (#9604) * Update MLST from 2.23 to 2.25 * test: update snapshots for mlst 2.25 --------- Co-authored-by: Subham Verma <[email protected]> * Update GitHub PR template check list item - version numbers (#9586) Update PR template check list item WRT version numbers Updating the PR template per the blog: ``` We are adopting topic channels to replace the versions.yml. For now both options are valid, but this will change. No more mixing of version channels. ``` Co-authored-by: Simon Pearce <[email protected]> * Ngscheckmate topics (#9597) * Start of topics conversion * Swap ngscheckmate to topic * Remove trailing whitespace * Update snapshots * Update test * Update snapshots * Skip two submodules on conda * Address comments * Update snapshot * Update snapshot --------- Co-authored-by: Louis Le Nézet <[email protected]> * Migrate samtools dict/faidx/merge to topics (#9598) * Update samtools dict/faidx/merge * Update subworkflows * Update meta * Update snapshots * Prettier * Add config back * Add config * Prettier * Allow `dream` to process non-formula contrasts (#9562) * Allow `dream` to process non-formula contrasts * Add test case without formula * Update `meta.yml` * Fix test with unstable file * Update subworkflow to allow non-formula contrasts with DREAM * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <[email protected]> * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <[email protected]> * Correct format of function * Fix contrast building and code flow * Update tests * Modify logic for contrast_string building * Make contrast_string compulsory with formula * Update tests * Refactor contrast_string construction logic Simplified the construction of contrast_string by removing unnecessary checks for treatment levels in the design matrix. * Make formula mutually exclusive to contrast tuple * Modify tests with mutually exclusive varaibles * Revert changes in first test case * Update tests * Fix tests --------- Co-authored-by: Copilot <[email protected]> * Add vcfpgloader/load module (#9579) * Add vcfpgloader/load module High-throughput VCF to PostgreSQL loader using asyncpg for bulk variant ingestion. * Remove throughput metric from meta.yml description * fix(vcfpgloader): fix CI failures for conda, singularity, and docker - Add pip as explicit conda dependency in environment.yml - Simplify container directive (remove oras:// for singularity compatibility) - Remove integration test requiring PostgreSQL database 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * chore: re-trigger CI for bioconda 0.5.3 propagation * chore: reorder deps to bust conda cache for 0.5.3 * fix: specify exact bioconda build string to force 0.5.3 * chore: sort environment.yml dependencies (linter) * fix: remove version from snapshot (varies by profile) * fix(vcfpgloader): restore version checking in tests Add back versions to snapshot assertions and update snapshot file with expected version output format for lint compliance. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * fix(vcfpgloader): use correct findAll pattern for topic versions Use process.out.findAll { key, val -> key.startsWith("versions")} pattern for topic-based versioning, matching nf-core conventions. Update snapshot with versions_vcfpgloader object format. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * feat(vcfpgloader): bump to v0.5.4 - Update environment.yml to bioconda::vcf-pg-loader=0.5.4 - Update container to ghcr.io/zacharyr41/vcf-pg-loader:0.5.4 - Add sed to parse version number from --version output - Update snapshot for 0.5.4 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * ci: retrigger after bioconda 0.5.4 merge * fix(vcfpgloader): update meta.yml version format Add type: eval and description to version command entries in outputs and topics sections. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * style(vcfpgloader): apply nextflow lint formatting * fix(vcfpgloader): add export to env() output variables Add explicit `export` to ROWS_LOADED assignments as recommended for env() output qualifiers. Note: `nextflow lint` still reports false positive errors for env() outputs - this is a known limitation of static analysis on shell scripts. The linter cannot verify variable definitions inside heredoc script blocks. Other nf-core modules (e.g., genescopefk) have the same lint warning. The code functions correctly at runtime. * Update modules/nf-core/vcfpgloader/load/tests/nextflow.config Co-authored-by: Famke Bäuerle <[email protected]> * chore(vcfpgloader): remove unused tags.yml * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * refactor(vcfpgloader): consolidate inputs into single tuple * feat(vcfpgloader): switch to BioContainers - Use BioContainers URLs instead of personal ghcr.io - Remove jq dependency, use Python for JSON parsing - Fix sed quoting for nf-core lint compatibility 🤖 Generated with [Claude Code](https://claude.ai/code) * fix(vcfpgloader): update snapshots to include row_count output Add missing row_count and log outputs to test snapshots to match the process outputs being asserted in tests. --------- Co-authored-by: Claude <[email protected]> Co-authored-by: Zachary Rothstein <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * Replace busybox with coreutils sort for genmod modules (#9610) Replace busybox with coreutils sort * Add error message * Update version * Fix output capture * Update tests * Update singularity container * Use https protocol --------- Co-authored-by: Louis Le Nézet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude Opus 4.5 <[email protected]> Co-authored-by: Evangelos Karatzas <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Jinn <[email protected]> Co-authored-by: ra25wog <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Jack Tierney <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: Rayan Hassaïne <[email protected]> Co-authored-by: Eduard Casas <[email protected]> Co-authored-by: root <[email protected]> Co-authored-by: root <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Eduard Casas <[email protected]> Co-authored-by: Felix Kummer <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Tatiana Gelaf Romer <[email protected]> Co-authored-by: Tatiana Gelaf Romer <[email protected]> Co-authored-by: Shubham Verma <[email protected]> Co-authored-by: Subham Verma <[email protected]> Co-authored-by: PeterKnealeCMRI <[email protected]> Co-authored-by: Delfina Terradas <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Zacharyr41 <[email protected]> Co-authored-by: Zachary Rothstein <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * Allow sample IDs to be integers with limma (#9615) * Allow bcftools sort to use 90% of allocated memory (#9611) * Allow bcftools sort to use all allocated memory * allow some overhead * Update vireo (#9599) * add two optional output files * add optional files to stub * add random seed to nextflow.config for consistency * hardcode random seed * Small bug fix for bff (#9600) bug fix * Add sentieon/hsmetrics (#9618) * Add sentieon/hsmetrics * Update meta and prettier * Update snapshot * Prettier * Swap picard/collecthsmetrics to topic (#9614) * Swap picard/collecthsmetrics to topic * Fix sed command * Update snapshot * Update subworkflow too * Apply suggestions from code review * chore: update snpeff to 5.4a and migrate to topics (#9621) * chore: update snpeff to 5.4a and migrate to topics * fix linting * fix linting * fix versions handling for snpeff and code polish * Update subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf * Swap mosdepth to topic (#9612) * Swap mosdepth to topic * Fail the test that should fail * Prettier * Update args check * chore: migrate ensemblvep to topics (#9624) * chore: migrate ensemblvep to topics * chore: fix versions usage * chore: fix linting * improve versions capture in tests * chore: update remaining snapshots * simplify versions capture thanks to @SPPearce * Modules hifi_trimmer (#9622) * Add hifitrimmer modules * Update versions to topic versions * Fix linting * Fix modules lint * Apply suggestions from code review Co-authored-by: Jim Downie <[email protected]> * Apply suggesttions and update snapshots * Simplify file name of filtered reads * Apply suggestions from code review Co-authored-by: Jim Downie <[email protected]> * Update test cases (update data location & remove redundant tests) --------- Co-authored-by: Jim Downie <[email protected]> * feat: add parse_null function and update filtering tests for minimum … (#9626) * feat: add parse_null function and update filtering tests for minimum abundance * style: fix linting * style: enhance docs in the code * Update modules/nf-core/custom/matrixfilter/templates/matrixfilter.R * Update versions and images for `nacho` modules (#9629) Update versions and tests * Add singularity definition to `nacho` modules (#9631) * Update versions and tests * Add singularity definition * Update basicpy (#9630) * Update basicpy The latest version of the tool works properly under Singularity and also offers control over the output filenames so we can use the standard ext.prefix or meta.id as the base name. * Update basicpy meta.yml * Round ffp file size in snapshot This is needed to account for normal output variation. * Fix nf-schema version for language server (#9636) * fix nf-schema version for language server * bump nextflow version * Make dream and limma work correctly with special characters (#9634) * multiqc: update containers to 1.33 (#9637) update containers to 1.33 * feat: samclip module (#8999) * feat: samclip module * fix: add nodefaults channel * fix: reviewer comments -> add samtools view + fixmate, emit bam, use Seqera container, update tests * fix: reviewer comments -> add samtools command args, cleanup, remove decompressed reference if made * fix: more reviewer comments (topics channel + emit one channel either BAM/CRAM) * Apply suggestions from code review Co-authored-by: Simon Pearce <[email protected]> * fix: remove versions * tests: fix snapshot (versions) --------- Co-authored-by: Simon Pearce <[email protected]> * fastq_qc_stats subworkflow update (#9643) * fastq_qc_stats subworkflow update - renamed and testing for skip all inputs case * bracket push * Update WHATSHAP/PHASE container, topic versions and task.cpus (#9642) * Add task.cpus in bgzip command and https for container. Fixed the new way of getting the version with topics * Add topics to meta * Updateing snapshot to correctly assess versions * Feature/localcdsearch (#9632) * local-cd-search annotate and download modules * Fixing lint * Update localcdsearch tool metadata in meta.yml * Fix container URL selection logic in main.nf * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Update modules/nf-core/localcdsearch/annotate/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> * Singularity container added * edamontology added * Updating test for one input only * Updating snap * Updating test for db downloding * Update version handling in main.nf * Update version expression in meta.yml * Refactor version handling in main.nf Updated version information to use a variable for better maintainability. * Update version retrieval expression in meta.yml * Add version information to stub Added version information for the tool in the main.nf file. * Add version information to stub Added version information to the main.nf file. * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: Evangelos Karatzas <[email protected]> * Refactor assertions to include process success check * Refactor assertions for process success in tests * Update container URL for local-cd-search * Remove redundant success assertion in tests --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Evangelos Karatzas <[email protected]> * Update RGI modules to be Nextflow strict syntax compliant (#9650) * 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]> * Make RGI modules syntax compliant --------- Co-authored-by: Simon Pearce <[email protected]> * Generate normalised matrix with `variancepartition/dream` (#9645) * Emit normalised matrix from dream and update tests * Update `meta.yml` * Fix linting error * Update snapshots * Bugfix * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests (#9521) * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests * Add ontologies to tcoffee/regressive and upp/align modules (#9484) * add ontologies to tcoffee regressive * add ontologies to upp align * Add module PBMARKDUP (#9457) * Add module pbmarkdup * Fix linting * Update path to test data * Update with code review (--dup-file, log, check file name collisions) * Fix linting * Update path to test data * Update modules/nf-core/pbmarkdup/meta.yml * Fix linting * Enable complex contrast strings in DESeq2 (#9473) * Enable complex contrast strings * Update docker image * Add test case with limma contrast string * Format changes and add test with shrinkage * Declare deepvariant optional html output (#9469) * Add deepvariant optional html * update snapshot * Update modules/nf-core/deepvariant/rundeepvariant/main.nf Co-authored-by: Ramprasad Neethiraj <[email protected]> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <[email protected]> * utils_nfcore_pipeline: fix small lang server error (#9492) fix small lang server error * Fix hisat2/align to support large genome indices (.ht2l) (#9493) HISAT2 uses .ht2l extension instead of .ht2 for large genomes. Updated index detection to match both extensions. Related to nf-core/rnaseq#1643 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude <[email protected]> * Update shinyngs modules to latest release (#9488) * Update semibin/singleeasybin environment (#9495) * add new ontology term to tcoffee align (#9497) * tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (#9489) * Sort file listing so "first" file is deterministic * Declare closure parameter per strict syntax Co-authored-by: Matthias Hörtenhuber <[email protected]> --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> * Sambamba depth add region bed input (#9498) * sambamba add region bed input * fix linting * fix linting * Apply suggestions from code review Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * fix fasta_index_methylseq and fastq_align_dedup workflows (#9496) * fix fasta_index_methylseq and fastq_align_dedup workflows for clarity and consistency - Updated variable names in fasta_index_methylseq to use 'channel' instead of 'Channel' for consistency. - Renamed UNTAR to UNTAR_BISMARK and UNTAR_BWAMETH for clarity in fasta_index_methylseq. - Enhanced comments and descriptions in meta.yml files for better understanding of input and output structures. - Adjusted test cases in fastq_align_dedup workflows to reflect changes in input structure from single-end to paired-end. - Updated version numbers in test snapshots to reflect recent changes. * fix: pre-commit lint fixes * Update test files for Glimpse (#9467) * Update glimpse * Update chunk * Update concordance * Revert changes * Fix glimpse test * Fix glimpse * Fix glimpse2 tests * Update sbwf * Remove old snapshots * Update glimpse * Update modules/nf-core/glimpse2/concordance/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update test --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * meta.yml schema: add `containers` section, fix order and simplify (#9503) * fix order * add container section * simplify schema * require https for singluarity * update and add topics to snakemake module (#9454) * update and add topics * add new topics structure * add stub test and capture version in snapshot * update to 9.14.0 * fix singularity be setting cache_dir * fix stub --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: mashehu <[email protected]> * fix sambamba depth stub version (#9509) * fix stub version * stray module * anota2seq: wrong variable name for batch assignment (#9511) rename variable * fix(anota2seq): add gene IDs and handle empty results (#9510) - Add missing gene_id_col parameter definition (defaults to 'gene_id') - Include gene IDs as first column in all results tables using configurable column name - Only write output files when there are significant results to avoid empty files - Mark all results TSV outputs as optional since they're conditionally created - Update test to use buffering results instead of empty mRNA_abundance results - Update test snapshots with new file formats including gene_id column This ensures anota2seq results are consistent with other modules and include gene identifiers for downstream analysis, while gracefully handling cases where no genes pass significance thresholds. Co-authored-by: Sebastian Uhrig <[email protected]> * fix(decoupler): reorder imports and ensure environment variables are … (#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules * Add strdrop/build (#9512) Add strdrop build * chore(deps): update infrastructural dependencies * 🔧 update image and bioconda container for VueGen to latest version (#9201) * 🔧 update image and bioconda container to latest version * ✅ update test snapshots * :bug: fix display of version of vuegen - had no command line interface option to display version, see https://github.com/Multiomics-Analytics-Group/vuegen/issues/167 * :art: display versions.yml content in snapshots * 🔧 add Dockerfile to install lastet PyPI vuegen version - does not pass hadolint(er) as of now * 🚧 add wave containers * :fire: remove README again * :fire: remove Dockerfile again * 🚧 try to follow Mahesh's advice * :bug: add explicit cache directory * 🔧 bump to Python 3.12 and remove channel prefix * :wrench: specify singularity image with https ... as specified in the docs: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers * 🚧 set user specified R libarary folder * ⏪ make docker and conda work again (using nf-core 3.5.1) * :wrench: switch again to custom docker image instead of wave - wave leads to too many custom installation issues * :bug: try to add font package * :fire: remove code moved to image - singularity runs in devcontainer * ⏪ add back conda quarto flag * :art: remove trailing whitespace * :art: format again * :art: hopefully the last trailing whitespace * :memo: document the build process and why the container is needed * Update image with nf-core one Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update container name Co-authored-by: Matthias Hörtenhuber <[email protected]> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * qsv/cat: bump version (#9518) Bump qsv * Update haplogrep3 recipe to use topics (#9523) Co-authored-by: nf-core-bot <[email protected]> * semibin/singleeasybin: bump version + migrate to topics (#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove unused folder * rename * trimmomatic revisit * cutadapt revisit * trimgalore revisit * bbduk revisit * fastp revisit * adapterremoval revisit * leehom checkpoint (#9534) * leehom checkpoint * debugged with transpose and proper collect on nf-test * leehom change order * remove ngmerge because cant deal with /1 /2 paired reads * paired end no merge test * New module: clusty (#9533) * new module clusty * patch links docs * fix prettier * remove non-mandatory input 'algorithm' * also patch stub input * Bump TRGT to 4.1.0 (#9514) * Bump TRGT to 4.1.0 * Switch to topics * Update modules/nf-core/trgt/genotype/tests/main.nf.test Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * fix missing quotes (#9535) * Fix dream to show more than 10 results (#9507) * fix: dream to show more than 10 results * test: update snapshots * test: update snapshots * feat: add round digits option and update snapshots again * fix: improve code formatting and update test snapshots * Fix tests and update snapshots * Update snapshot for `abundance_differential_filter` subworkflow * Fix tests with unstable content * Fix unstable files in test for `abundance_differential_filter` subworkflow --------- Co-authored-by: Anabella Trigila <[email protected]> * rename to more appropriate fastq_preprocess_seqkit (#9537) * New module - TD2 (added modules for td2.longorfs & td2.predict) (#9475) * added modules for td2.longorfs & td2.predict * changes to version handling, updated snaps, and tests - resolving comments * added topics section in meta.yml * fix topics section in meta.yml * Update modules/nf-core/td2/longorfs/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Update main.nf - stub run * Update meta.yml * resolving comments * updated emad ontologies * Update modules/nf-core/td2/predict/tests/main.nf.test.snap * Update modules/nf-core/td2/predict/main.nf * Update modules/nf-core/td2/longorfs/tests/main.nf.test.snap * Update modules/nf-core/td2/longorfs/main.nf * Update modules/nf-core/td2/predict/tests/main.nf.test.snap * Update modules/nf-core/td2/longorfs/tests/main.nf.test.snap --------- Co-authored-by: Simon Pearce <[email protected]> * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (#9531) * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(https://github.com/GavinHaLab/ichorCNA/pull/26). It is unclear when a new version will be out, so I have patched the current bioconda package (https://github.com/bioconda/bioconda-recipes/pull/61045) and built new container images, which I want to update to in this PR. * Update some md5sums * Update test snapshot * Update test snapshot * RSeQC split_bam.py module implementation (#9536) * RSeQC split_bam.py module implementation Syntax edit Refractored version channel to topic Cleanup * Update modules/nf-core/rseqc/splitbam/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Updated snapshot --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * remove topics from multiqc (#9530) * remove topics from multiqc * versions_multiqc -> versions * Apply suggestion from @nvnieuwk * fix meta.yml after merge * bump to MultiQC version 1.33 (#9538) * bump to 1.33 * update snapshots --------- Co-authored-by: Matthias Hörtenhuber <[email protected]> * Add strdrop/call (#9513) * Add strdrop build * Add strdrop/call * remove tag * fix wrong parameter name in error * align * remove duplicate versions * snaps * figure out why snapshots are not stable * different versions of trgt used in setup * Bump TRGT to 5.0.0 (#9541) 5.0.0 * Channel -> channel in some subwfs (#9542) Channel -> channel * Migrate cat/fastq to topic channel (#9543) * Migrate cat/fastq to topic channel * Remove out.versions in related subworkflows * Update snapshots (again) * Add module picard/collectvariantcallingmetrics (#9502) * Add module picard/collectvariantcallingmetrics * Run prettier * Fix format * Make one input tuple * Change test input structure * Add md5 checksum * Update snapshot * Update meta.yml * Support multithreading * Remove TODO Co-authored-by: Famke Bäuerle <[email protected]> --------- Co-authored-by: Famke Bäuerle <[email protected]> * fix tabix/tabix stub (#9544) * fix tabix stub * bump max shards to 16 * Unify msa modules (#9539) * add mafft_align subworkflow to prepare channels for mafft/align like all other msa modules * default output format fasta for tcoffee align and regressive to match other msa modules * [automated] Fix linting with Prettier * Update subworkflows/nf-core/mafft_align/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> --------- Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Fix missing version from subworkflow snapshot (#9548) * New module: whatshap/phase (#9431) * add whatshap phase module * change the vcf-specific test * change test * add versions * remove snapshot * update snapshot * Update modules/nf-core/whatshap/phase/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * rm unused args * add snapshot * add ontologies * update the snapshot * add versions to snapshot * fix stub issues * update the test and snap * fix format with "nextflow lint" * fix hardcoded name and file name ambiguity problem --------- Co-authored-by: Famke Bäuerle <[email protected]> * Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (#9549) * bump version cat/cat * reinclude cat tags for other modules * patch test name & meta.yml * Update main.nf.test * plastid metagene_generate, make_wiggle, psite (#9482) * plastid metagene_generate, make_wiggle, psite * pair BAM and BAI files * pair bam and p_offsets * omit optional arguments * metagene generate accepts various input formats * add meta * do not remove variable headers from output files * warning about hard-coded version * make lint happy * make lint happy #2 * plastid/make_wiggle: nf-core standards compliance - Add mapping_rule val input (enum: fiveprime, threeprime, center, fiveprime_variable) - Move output_format to ext.args (optional arg per nf-core standards) - Add validation: error if p_offsets missing with fiveprime_variable - Remove hardcoded --fiveprime_variable - Update meta.yml with mapping_rule input and enum - Update tests with mapping_rule input 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * adapt meta.yml to new parameters * plastid: consolidate test snapshots and fix reproducibility - Consolidate multiple snapshot assertions into single snapshots per test - Remove snapshots of empty stub files (just check existence) - Exclude non-reproducible PNG from psite snapshots (matplotlib drift) - Format metagene_generate command across multiple lines 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * plastid/make_wiggle: remove tracks from snapshot Wig files have non-reproducible md5sums across environments. Content is already validated via getText().contains('track'). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> * plastid/psite: remove non-reproducible outputs from snapshot metagene_profiles.txt and p_offsets.txt have non-reproducible md5sums. Content is already validated via getText().contains() checks. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]> --------- Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Claude Opus 4.5 <[email protected]> * Add index and threads to trgt/merge (#9545) * Fix test path modification (#9465) * Update bcftools * Update bcftools csq * Update somalier ancestry * Update bcftools pluginfilltags * Update cnvnator * Update snap cnvnator * Fix extract somalier sbwf * Update snapshot * Update md5 * Fix linting * Upd snapshot * Upd snapshot * Upd snapshot * Upd snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update xenium ranger modules and subworkflows (#9525) * update xeniumranger modules to use xeniumranger v4.0 * update xeniumranger modules to use xeniumranger v4.0 * fix: update xeniumranger import-segmentation tests and logic * update test compute resource spec to follow 10x website * remove extra file * fix: apply topic channels and update meta.yml structure for xeniumranger * fix: update meta.yml structure to satisfy schema * fix: align meta.yml with topic versions blog post example * fix: update meta.yml topics structure to satisfy schema validation * fix: automated lint fix for meta.yml topics structure * fix: use standard container definition syntax * fix: apply topic versions to rename module * fix: apply topic versions and meta.yml schema fixes for xeniumranger modules and subworkflows * untrack files * remove test config files for github workflow * remove config def in tests * remove config def in tests * Update tests and snapshots for xeniumranger modules and subworkflows * remove subworkflows for xeniumranger * remove subworkflows for xeniumranger * fix: update test template * fix relabel meta.yml * make prek hppy * make prek hppy * make prek hppy * update import-segmentation doc * update import-segmentation doc * fix oncologies * Fix snapshot file key order for rename and resegment modules * Apply suggestions from code review Co-authored-by: Copilot <[email protected]> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <[email protected]> Co-authored-by: Sameesh Kher <[email protected]> Co-authored-by: Copilot <[email protected]> * Version update: Modkit repair, callmods and bedmethyltobigwig (#9547) * update to v0.6 * update to v0.6 * update to v0.6 * update yml * update to v0.6 * update snapshot * update snapshot --------- Co-authored-by: ra25wog <[email protected]> * Update `GLIMPSE` sbwf (#9524) * Update glimpse sbwf * Update test * Update filter operation * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add quilt imputation subworkflow (#9443) * Add sbwf quilt * Fix tags * Update meta * Use modules repo files * Update glimpse2 imputation subworkflow (#9434) * Update glimpse2 sbwf * Update test * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf Co-authored-by: Jonathan Manning <[email protected]> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <[email protected]> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> * Add `BEAGLE5` imputation subworkflow (#9550) * Update glimpse2 sbwf * Update test * Add region to beagle5 * Add subworkflow * Fix linting * Fix linting * Fix linting * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add comment * Update grouping and test * Remove tag * Revert change glimpse2 reference * Revert change glimpse2 sbwf * Revert change glimpse2 sbwf * Revert change glimpse2 sbwf --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add minimac4 imputation subworkfllow (#9451) * Add vcf_impute_minimac4 * Update linting * Update test * Fix linting * Update minimac4 sbwf * Remove tag * Remove tag * Fix linting * Add comment * Update snapshot * Fix nf-test * Add BBSplit stats to MultiQC in fastq_qc_trim_filter_setstrandedness subworkflow (#9559) Add BBSplit stats to MultiQC files in fastq_qc_trim_filter_setstrandedness Pass BBSplit stats output to MultiQC for visualization of read binning statistics. MultiQC 1.33+ includes support for parsing BBSplit stats.txt files and displaying per-sample read distribution across reference genomes. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <[email protected]> * Update cutadapt (#9551) * proper stub for gz and stub test added * topic output syntax and tests update * meta yml updated with topics and ontologies * meta file curated * version bump to latest * update nf-tests properly * adding self to maintainers * removed Z flag as is deprecated after v4.10 * conda bug with different pre-built python version fixed * added cutadapt to stub now that stub gz is properly created, and removed cutadapt versions, since it is now ported to topics * single-end test with tool skips * Standarize and alignment for all imputation and alignment modules (#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <[email protected]> * Update Infrastructural dependencies * Remove .view() (#9567) * Bump strdrop to 0.3.1 (#9565) * Remove unecessary tags (#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics…

Joon-Klaps added 3 commits December 10, 2025 16:27

bump version cat/cat

6c21e57

reinclude cat tags for other modules

cc7dfd4

Merge branch 'master' into cat/cat

1e870a2

mashehu approved these changes Dec 10, 2025

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Joon-Klaps added 3 commits December 10, 2025 17:05

patch test name & meta.yml

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Merge branch 'cat/cat' of https://github.com/Joon-Klaps/modules into …

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…cat/cat

Update main.nf.test

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Joon-Klaps enabled auto-merge December 10, 2025 18:17

Joon-Klaps added this pull request to the merge queue Dec 10, 2025

Merged via the queue into nf-core:master with commit 69614d4 Dec 10, 2025
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Joon-Klaps deleted the cat/cat branch December 10, 2025 18:22

vagkaratzas pushed a commit that referenced this pull request Dec 12, 2025

Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (#…

196f22c

…9549) * bump version cat/cat * reinclude cat tags for other modules * patch test name & meta.yml * Update main.nf.test

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Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel #9549

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Joon-Klaps commented Dec 10, 2025

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Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel #9549

Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel #9549

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Joon-Klaps commented Dec 10, 2025

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