Update `Modkit pileup` by jkh00 · Pull Request #9553 · nf-core/modules

jkh00 · 2025-12-11T12:59:20Z

Bump modkit pileup version from v0.5.0 -> v0.6.0

Couple of flags were removed or changed in the v0.6.0 version, details [here].(https://nanoporetech.github.io/modkit/migrating_060.html)

New changes:

In this module, modkit pileup by default output bgzf-compressed bedmethyl.
--bedgraph flag is removed.
--partition-tags changed to --phased
updated main.nf.test to test the new params
added TABIX_BGZIP module into bedmethyltobigwig main.nf.test to decompress pileup output before piping into bedmethyltobigwig.

PR checklist

Closes #XXX

jkh00 · 2025-12-11T13:04:47Z

@nf-core-bot fix linting

github-actions · 2025-12-11T13:05:34Z

Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

jkh00 · 2025-12-11T14:58:16Z

seems like theres some problems on github site for the test runs

modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test

modules/nf-core/modkit/bedmethyltobigwig/tests/decompressed.config

modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test

modules/nf-core/modkit/pileup/main.nf

Joon-Klaps · 2025-12-12T08:52:33Z

modules/nf-core/modkit/pileup/tests/main.nf.test

@@ -64,38 +64,7 @@ nextflow_process {

    test("[bam, bai], [fasta, fai], bed") {


Does the module not run without a config anymore or? Why was this test removed?

currently in this v0.6 version, --include-bed param requires either --motif or --modified-bases. I ran into an error if neither of these were supplied:

Error! currently, --include-bed requires a --motif or --modified-bases. This limitation may be removed in the future.

Joon-Klaps · 2025-12-12T08:54:11Z

modules/nf-core/modkit/pileup/tests/nextflow.5mC_5hmC.config

Please merge all the configs into one and use the module_args params to specify which arguments are to be given inside the main.nf.test

I'm not quite sure how to do this, could you give some examples/ guides?

oh wait, think I found the docs, I will give it a go :)

Joon-Klaps · 2025-12-12T08:55:08Z

@jkh00 Great work, some minor comments! Let me know if I was unclear.

jkh00 · 2025-12-12T10:49:38Z

@nf-core-bot fix linting

jkh00 · 2025-12-12T11:52:15Z

@Joon-Klaps thanks a lot for the suggestions! I have implemented them :))

Joon-Klaps

Awesome! Thx!

* 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re>

* 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * 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 <louislenezet@gmaio.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re>

* testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* 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 <noreply@anthropic.com> * 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * 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 <louislenezet@gmaio.com> * 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * 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 <louislenezet@gmaio.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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: nf-core/test-datasets#1820 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * Add schema reference to ribocode/ribocode meta.yml 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <root@ip-172-31-44-88.us-west-2.compute.internal> Co-authored-by: root <root@ip-172-31-20-12.us-west-2.compute.internal> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Eduard Casas <eduard.casas@WMG-FN0Q7KY4X6.local> * 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 <noreply@anthropic.com> * 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 <felix.kummer@hu-berlin.de> * harshil --------- Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * 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 <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <romert01@pfizer.com> * 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 <subhamverma@S.local> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> * 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 <175728472+Copilot@users.noreply.github.com> * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 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 <175728472+Copilot@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <45968370+famosab@users.noreply.github.com> * chore(vcfpgloader): remove unused tags.yml * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <noreply@anthropic.com> Co-authored-by: Zachary Rothstein <zacharyr41@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Jack Tierney <43453737+JackCurragh@users.noreply.github.com> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Eduard Casas <123982193+eduard-watchmaker@users.noreply.github.com> Co-authored-by: root <root@ip-172-31-44-88.us-west-2.compute.internal> Co-authored-by: root <root@ip-172-31-20-12.us-west-2.compute.internal> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Eduard Casas <eduard.casas@WMG-FN0Q7KY4X6.local> Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Tatiana Gelaf Romer <tatiana.gelafromer@pfizer.com> Co-authored-by: Tatiana Gelaf Romer <romert01@pfizer.com> Co-authored-by: Shubham Verma <58583530+svermai@users.noreply.github.com> Co-authored-by: Subham Verma <subhamverma@S.local> Co-authored-by: PeterKnealeCMRI <130641023+PeterKnealeCMRI@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Zacharyr41 <zrothstein@uchicago.edu> Co-authored-by: Zachary Rothstein <zacharyr41@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

@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 <20065894+ramprasadn@users.noreply.github.com> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <mashehu@users.noreply.github.com> --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * 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 <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * Update test --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * 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 <suhrig@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * Update container name Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * qsv/cat: bump version (#9518) Bump qsv * Update haplogrep3 recipe to use topics (#9523) Co-authored-by: nf-core-bot <core@nf-co.re> * semibin/singleeasybin: bump version + migrate to topics (#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <18577080+atrigila@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated snapshot --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <kadomu@gmail.com> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * 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 <louislenezet@gmaio.com> * 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 <175728472+Copilot@users.noreply.github.com> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 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 <jin.khoo@campus.lmu.de> * 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 <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <pininforthefjords@gmail.com> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> * 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 <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <louislenezet@gmaio.com> * 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * 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 <louislenezet@gmaio.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: vagkaratzas <vagelaros.gee@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

@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 <20065894+ramprasadn@users.noreply.github.com> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <mashehu@users.noreply.github.com> --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * 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 <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * Update test --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * 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 <suhrig@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * Update container name Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * qsv/cat: bump version (#9518) Bump qsv * Update haplogrep3 recipe to use topics (#9523) Co-authored-by: nf-core-bot <core@nf-co.re> * semibin/singleeasybin: bump version + migrate to topics (#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <18577080+atrigila@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated snapshot --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <kadomu@gmail.com> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * 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 <louislenezet@gmaio.com> * 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 <175728472+Copilot@users.noreply.github.com> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 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 <jin.khoo@campus.lmu.de> * 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 <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <pininforthefjords@gmail.com> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> * 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 <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <louislenezet@gmaio.com> * 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * 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 <louislenezet@gmaio.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: vagkaratzas <vagelaros.gee@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* 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 (nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cutadapt (nf-core#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 (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (nf-core#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * RiboCode - prepare_transcripts, metaplots, ribocode (nf-core#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: nf-core/test-datasets#1820 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * Add schema reference to ribocode/ribocode meta.yml 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Revert nf-test.config to standard test-datasets paths test-datasets PR nf-core#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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * Bump stranger (nf-core#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 (nf-core#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 (nf-core#9572) * Rseqc add bam index - topics-based versions - version bump (nf-core#9546) * Updated rseqc/bamstat: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/inferexperiment: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/innerdistance: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/junctionannotation: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/junctionsaturation: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/readdistribution: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/readduplication: Added BAI support per nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cmaple (nf-core#9580) * adding uncompression functionality * new versions output syntax * meta.yml updated * Add fq2bam fq align dd bwamem (nf-core#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 <root@ip-172-31-44-88.us-west-2.compute.internal> Co-authored-by: root <root@ip-172-31-20-12.us-west-2.compute.internal> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Eduard Casas <eduard.casas@WMG-FN0Q7KY4X6.local> * Update RSEQC modules with Seqera Wave containers matching environment.yml (nf-core#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 <noreply@anthropic.com> * Allow gzipped inputs to modkit/bedmethyltobigwig (nf-core#9591) * Allow gzipped inputs to modkit/bedmethyltobigwig * Update modules/nf-core/modkit/bedmethyltobigwig/main.nf Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> * harshil --------- Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> * Fix modkit pileup stub (nf-core#9590) * feat(ribowaltz): Export underlying data from QC plots (nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * feat(ribowaltz): Export underlying data for all QC plots (nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * chore(deps): update conda-incubator/setup-miniconda digest to 8352349 * Swap bcftools/mpileup to topic (nf-core#9596) * Swap bcftools/mpileup to topic * Fix linting * Update snapshots * Swap mpileup to topics (nf-core#9595) * Swap mpileup to topics * Apply suggestions from code review * Add Harshil back as author * Update snapshots * Fix string path (nf-core#9602) * Fix string path * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Bump genmod to 3.10.2 and switch to topics (nf-core#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 (nf-core#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 <romert01@pfizer.com> * Update MLST from 2.23 to 2.25 (nf-core#9604) * Update MLST from 2.23 to 2.25 * test: update snapshots for mlst 2.25 --------- Co-authored-by: Subham Verma <subhamverma@S.local> * Update GitHub PR template check list item - version numbers (nf-core#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 <24893913+SPPearce@users.noreply.github.com> * Ngscheckmate topics (nf-core#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 <58640615+LouisLeNezet@users.noreply.github.com> * Migrate samtools dict/faidx/merge to topics (nf-core#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 (nf-core#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 <175728472+Copilot@users.noreply.github.com> * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 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 <175728472+Copilot@users.noreply.github.com> * Add vcfpgloader/load module (nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <45968370+famosab@users.noreply.github.com> * chore(vcfpgloader): remove unused tags.yml * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <noreply@anthropic.com> Co-authored-by: Zachary Rothstein <zacharyr41@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Replace busybox with coreutils sort for genmod modules (nf-core#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 <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Jack Tierney <43453737+JackCurragh@users.noreply.github.com> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Eduard Casas <123982193+eduard-watchmaker@users.noreply.github.com> Co-authored-by: root <root@ip-172-31-44-88.us-west-2.compute.internal> Co-authored-by: root <root@ip-172-31-20-12.us-west-2.compute.internal> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Eduard Casas <eduard.casas@WMG-FN0Q7KY4X6.local> Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Tatiana Gelaf Romer <tatiana.gelafromer@pfizer.com> Co-authored-by: Tatiana Gelaf Romer <romert01@pfizer.com> Co-authored-by: Shubham Verma <58583530+svermai@users.noreply.github.com> Co-authored-by: Subham Verma <subhamverma@S.local> Co-authored-by: PeterKnealeCMRI <130641023+PeterKnealeCMRI@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Zacharyr41 <zrothstein@uchicago.edu> Co-authored-by: Zachary Rothstein <zacharyr41@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

@mashehu

…f-core#9521) * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests * Add ontologies to tcoffee/regressive and upp/align modules (nf-core#9484) * add ontologies to tcoffee regressive * add ontologies to upp align * Add module PBMARKDUP (nf-core#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 (nf-core#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 (nf-core#9469) * Add deepvariant optional html * update snapshot * Update modules/nf-core/deepvariant/rundeepvariant/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * utils_nfcore_pipeline: fix small lang server error (nf-core#9492) fix small lang server error * Fix hisat2/align to support large genome indices (.ht2l) (nf-core#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 <noreply@anthropic.com> * Update shinyngs modules to latest release (nf-core#9488) * Update semibin/singleeasybin environment (nf-core#9495) * add new ontology term to tcoffee align (nf-core#9497) * tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (nf-core#9489) * Sort file listing so "first" file is deterministic * Declare closure parameter per strict syntax Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * Sambamba depth add region bed input (nf-core#9498) * sambamba add region bed input * fix linting * fix linting * Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix fasta_index_methylseq and fastq_align_dedup workflows (nf-core#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 (nf-core#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 <mashehu@users.noreply.github.com> * Update test --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * meta.yml schema: add `containers` section, fix order and simplify (nf-core#9503) * fix order * add container section * simplify schema * require https for singluarity * update and add topics to snakemake module (nf-core#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 <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * fix sambamba depth stub version (nf-core#9509) * fix stub version * stray module * anota2seq: wrong variable name for batch assignment (nf-core#9511) rename variable * fix(anota2seq): add gene IDs and handle empty results (nf-core#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 <suhrig@users.noreply.github.com> * fix(decoupler): reorder imports and ensure environment variables are … (nf-core#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules * Add strdrop/build (nf-core#9512) Add strdrop build * chore(deps): update infrastructural dependencies * 🔧 update image and bioconda container for VueGen to latest version (nf-core#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 <mashehu@users.noreply.github.com> * Update container name Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * qsv/cat: bump version (nf-core#9518) Bump qsv * Update haplogrep3 recipe to use topics (nf-core#9523) Co-authored-by: nf-core-bot <core@nf-co.re> * semibin/singleeasybin: bump version + migrate to topics (nf-core#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * remove unused folder * rename * trimmomatic revisit * cutadapt revisit * trimgalore revisit * bbduk revisit * fastp revisit * adapterremoval revisit * leehom checkpoint (nf-core#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 (nf-core#9533) * new module clusty * patch links docs * fix prettier * remove non-mandatory input 'algorithm' * also patch stub input * Bump TRGT to 4.1.0 (nf-core#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 <mashehu@users.noreply.github.com> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix missing quotes (nf-core#9535) * Fix dream to show more than 10 results (nf-core#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 <18577080+atrigila@users.noreply.github.com> * rename to more appropriate fastq_preprocess_seqkit (nf-core#9537) * New module - TD2 (added modules for td2.longorfs & td2.predict) (nf-core#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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (nf-core#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 (nf-core#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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated snapshot --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * remove topics from multiqc (nf-core#9530) * remove topics from multiqc * versions_multiqc -> versions * Apply suggestion from @nvnieuwk * fix meta.yml after merge * bump to MultiQC version 1.33 (nf-core#9538) * bump to 1.33 * update snapshots --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Add strdrop/call (nf-core#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 (nf-core#9541) 5.0.0 * Channel -> channel in some subwfs (nf-core#9542) Channel -> channel * Migrate cat/fastq to topic channel (nf-core#9543) * Migrate cat/fastq to topic channel * Remove out.versions in related subworkflows * Update snapshots (again) * Add module picard/collectvariantcallingmetrics (nf-core#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 <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * fix tabix/tabix stub (nf-core#9544) * fix tabix stub * bump max shards to 16 * Unify msa modules (nf-core#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 <kadomu@gmail.com> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Fix missing version from subworkflow snapshot (nf-core#9548) * New module: whatshap/phase (nf-core#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 <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (nf-core#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 (nf-core#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 nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * Add index and threads to trgt/merge (nf-core#9545) * Fix test path modification (nf-core#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 <louislenezet@gmaio.com> * Update xenium ranger modules and subworkflows (nf-core#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 <175728472+Copilot@users.noreply.github.com> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Version update: Modkit repair, callmods and bedmethyltobigwig (nf-core#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 <jin.khoo@campus.lmu.de> * Update `GLIMPSE` sbwf (nf-core#9524) * Update glimpse sbwf * Update test * Update filter operation * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add quilt imputation subworkflow (nf-core#9443) * Add sbwf quilt * Fix tags * Update meta * Use modules repo files * Update glimpse2 imputation subworkflow (nf-core#9434) * Update glimpse2 sbwf * Update test * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add `BEAGLE5` imputation subworkflow (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> * 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 <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add minimac4 imputation subworkfllow (nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cutadapt (nf-core#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 (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (nf-core#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: vagkaratzas <vagelaros.gee@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

@mashehu

* fastq_shortreads_preprocess_qc init * skip all nf-test init * fastq_qc_stats subworkflow update (#9643) * fastq_qc_stats subworkflow update - renamed and testing for skip all inputs case * bracket push * empty skip all test working * meta init * seqera ai filled inputs and outputs of meta * stub added * sarscov2 - fastq - seqfu - seqkit - deacon - single_end nf-test added * prinseqplusplus added * clumpify added, cat_fastq added, nf-test added for missing tools * 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 <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <32259775+vagkaratzas@users.noreply.github.com> * 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 <jfy133@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Make RGI modules syntax compliant --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <20065894+ramprasadn@users.noreply.github.com> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <mashehu@users.noreply.github.com> --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * 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 <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * Update test --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * 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 <suhrig@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * Update container name Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * qsv/cat: bump version (#9518) Bump qsv * Update haplogrep3 recipe to use topics (#9523) Co-authored-by: nf-core-bot <core@nf-co.re> * semibin/singleeasybin: bump version + migrate to topics (#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * 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 <18577080+atrigila@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * 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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated snapshot --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <mashehu@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <kadomu@gmail.com> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * 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 <louislenezet@gmaio.com> * 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 <175728472+Copilot@users.noreply.github.com> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 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 <jin.khoo@campus.lmu.de> * 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 <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <pininforthefjords@gmail.com> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> * 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 <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <noreply@anthropic.com> * 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 <louislenezet@gmaio.com> * 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * 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 <louislenezet@gmaio.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: vagkaratzas <vagelaros.gee@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * FASTQ_REMOVEADAPTERS_MERGE added * paired-end, adapterremoval test added * adapterremoval test * comment removed * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * adapter removal and merge params added to meta.yml * comment updated * fastq_complexity_filter added, nf-tests udpated, meta.yml updated * variable renames * dedupe flag for clumpify * check if deterministic output * updating non-deterministic snapshot * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * warning message added in subworkflow's description, regarding required process configurations * CAT_FASTQ logic update --------- Co-authored-by: EliottBo <112384714+eliottBo@users.noreply.github.com> Co-authored-by: Alejandra Escobar <ales@ebi.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Kateryna Nemesh <121881939+kornkv@users.noreply.github.com> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>

* 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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re>

* testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>

* 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 (nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cutadapt (nf-core#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 (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (nf-core#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * RiboCode - prepare_transcripts, metaplots, ribocode (nf-core#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: nf-core/test-datasets#1820 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * Add schema reference to ribocode/ribocode meta.yml 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Revert nf-test.config to standard test-datasets paths test-datasets PR nf-core#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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * Bump stranger (nf-core#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 (nf-core#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 (nf-core#9572) * Rseqc add bam index - topics-based versions - version bump (nf-core#9546) * Updated rseqc/bamstat: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/inferexperiment: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/innerdistance: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/junctionannotation: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/junctionsaturation: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/readdistribution: Added BAI support per nf-core#9460 & topics-based versions * Updated rseqc/readduplication: Added BAI support per nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cmaple (nf-core#9580) * adding uncompression functionality * new versions output syntax * meta.yml updated * Add fq2bam fq align dd bwamem (nf-core#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 <root@ip-172-31-44-88.us-west-2.compute.internal> Co-authored-by: root <root@ip-172-31-20-12.us-west-2.compute.internal> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Eduard Casas <eduard.casas@WMG-FN0Q7KY4X6.local> * Update RSEQC modules with Seqera Wave containers matching environment.yml (nf-core#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 <noreply@anthropic.com> * Allow gzipped inputs to modkit/bedmethyltobigwig (nf-core#9591) * Allow gzipped inputs to modkit/bedmethyltobigwig * Update modules/nf-core/modkit/bedmethyltobigwig/main.nf Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> * harshil --------- Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> * Fix modkit pileup stub (nf-core#9590) * feat(ribowaltz): Export underlying data from QC plots (nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * feat(ribowaltz): Export underlying data for all QC plots (nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * chore(deps): update conda-incubator/setup-miniconda digest to 8352349 * Swap bcftools/mpileup to topic (nf-core#9596) * Swap bcftools/mpileup to topic * Fix linting * Update snapshots * Swap mpileup to topics (nf-core#9595) * Swap mpileup to topics * Apply suggestions from code review * Add Harshil back as author * Update snapshots * Fix string path (nf-core#9602) * Fix string path * Update subworkflows/nf-core/vcf_impute_beagle5/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Bump genmod to 3.10.2 and switch to topics (nf-core#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 (nf-core#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 <romert01@pfizer.com> * Update MLST from 2.23 to 2.25 (nf-core#9604) * Update MLST from 2.23 to 2.25 * test: update snapshots for mlst 2.25 --------- Co-authored-by: Subham Verma <subhamverma@S.local> * Update GitHub PR template check list item - version numbers (nf-core#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 <24893913+SPPearce@users.noreply.github.com> * Ngscheckmate topics (nf-core#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 <58640615+LouisLeNezet@users.noreply.github.com> * Migrate samtools dict/faidx/merge to topics (nf-core#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 (nf-core#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 <175728472+Copilot@users.noreply.github.com> * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 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 <175728472+Copilot@users.noreply.github.com> * Add vcfpgloader/load module (nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <45968370+famosab@users.noreply.github.com> * chore(vcfpgloader): remove unused tags.yml * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * 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 <noreply@anthropic.com> Co-authored-by: Zachary Rothstein <zacharyr41@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Replace busybox with coreutils sort for genmod modules (nf-core#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 <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Jack Tierney <43453737+JackCurragh@users.noreply.github.com> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Eduard Casas <123982193+eduard-watchmaker@users.noreply.github.com> Co-authored-by: root <root@ip-172-31-44-88.us-west-2.compute.internal> Co-authored-by: root <root@ip-172-31-20-12.us-west-2.compute.internal> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Eduard Casas <eduard.casas@WMG-FN0Q7KY4X6.local> Co-authored-by: Felix Kummer <felix.kummer@hu-berlin.de> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Tatiana Gelaf Romer <tatiana.gelafromer@pfizer.com> Co-authored-by: Tatiana Gelaf Romer <romert01@pfizer.com> Co-authored-by: Shubham Verma <58583530+svermai@users.noreply.github.com> Co-authored-by: Subham Verma <subhamverma@S.local> Co-authored-by: PeterKnealeCMRI <130641023+PeterKnealeCMRI@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Zacharyr41 <zrothstein@uchicago.edu> Co-authored-by: Zachary Rothstein <zacharyr41@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

@mashehu

…f-core#9521) * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests * Add ontologies to tcoffee/regressive and upp/align modules (nf-core#9484) * add ontologies to tcoffee regressive * add ontologies to upp align * Add module PBMARKDUP (nf-core#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 (nf-core#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 (nf-core#9469) * Add deepvariant optional html * update snapshot * Update modules/nf-core/deepvariant/rundeepvariant/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * utils_nfcore_pipeline: fix small lang server error (nf-core#9492) fix small lang server error * Fix hisat2/align to support large genome indices (.ht2l) (nf-core#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 <noreply@anthropic.com> * Update shinyngs modules to latest release (nf-core#9488) * Update semibin/singleeasybin environment (nf-core#9495) * add new ontology term to tcoffee align (nf-core#9497) * tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (nf-core#9489) * Sort file listing so "first" file is deterministic * Declare closure parameter per strict syntax Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * Sambamba depth add region bed input (nf-core#9498) * sambamba add region bed input * fix linting * fix linting * Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix fasta_index_methylseq and fastq_align_dedup workflows (nf-core#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 (nf-core#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 <mashehu@users.noreply.github.com> * Update test --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * meta.yml schema: add `containers` section, fix order and simplify (nf-core#9503) * fix order * add container section * simplify schema * require https for singluarity * update and add topics to snakemake module (nf-core#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 <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * fix sambamba depth stub version (nf-core#9509) * fix stub version * stray module * anota2seq: wrong variable name for batch assignment (nf-core#9511) rename variable * fix(anota2seq): add gene IDs and handle empty results (nf-core#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 <suhrig@users.noreply.github.com> * fix(decoupler): reorder imports and ensure environment variables are … (nf-core#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules * Add strdrop/build (nf-core#9512) Add strdrop build * chore(deps): update infrastructural dependencies * 🔧 update image and bioconda container for VueGen to latest version (nf-core#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 <mashehu@users.noreply.github.com> * Update container name Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * qsv/cat: bump version (nf-core#9518) Bump qsv * Update haplogrep3 recipe to use topics (nf-core#9523) Co-authored-by: nf-core-bot <core@nf-co.re> * semibin/singleeasybin: bump version + migrate to topics (nf-core#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * remove unused folder * rename * trimmomatic revisit * cutadapt revisit * trimgalore revisit * bbduk revisit * fastp revisit * adapterremoval revisit * leehom checkpoint (nf-core#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 (nf-core#9533) * new module clusty * patch links docs * fix prettier * remove non-mandatory input 'algorithm' * also patch stub input * Bump TRGT to 4.1.0 (nf-core#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 <mashehu@users.noreply.github.com> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix missing quotes (nf-core#9535) * Fix dream to show more than 10 results (nf-core#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 <18577080+atrigila@users.noreply.github.com> * rename to more appropriate fastq_preprocess_seqkit (nf-core#9537) * New module - TD2 (added modules for td2.longorfs & td2.predict) (nf-core#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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (nf-core#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 (nf-core#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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated snapshot --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * remove topics from multiqc (nf-core#9530) * remove topics from multiqc * versions_multiqc -> versions * Apply suggestion from @nvnieuwk * fix meta.yml after merge * bump to MultiQC version 1.33 (nf-core#9538) * bump to 1.33 * update snapshots --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Add strdrop/call (nf-core#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 (nf-core#9541) 5.0.0 * Channel -> channel in some subwfs (nf-core#9542) Channel -> channel * Migrate cat/fastq to topic channel (nf-core#9543) * Migrate cat/fastq to topic channel * Remove out.versions in related subworkflows * Update snapshots (again) * Add module picard/collectvariantcallingmetrics (nf-core#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 <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * fix tabix/tabix stub (nf-core#9544) * fix tabix stub * bump max shards to 16 * Unify msa modules (nf-core#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 <kadomu@gmail.com> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Fix missing version from subworkflow snapshot (nf-core#9548) * New module: whatshap/phase (nf-core#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 <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (nf-core#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 (nf-core#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 nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * Add index and threads to trgt/merge (nf-core#9545) * Fix test path modification (nf-core#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 <louislenezet@gmaio.com> * Update xenium ranger modules and subworkflows (nf-core#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 <175728472+Copilot@users.noreply.github.com> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Version update: Modkit repair, callmods and bedmethyltobigwig (nf-core#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 <jin.khoo@campus.lmu.de> * Update `GLIMPSE` sbwf (nf-core#9524) * Update glimpse sbwf * Update test * Update filter operation * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add quilt imputation subworkflow (nf-core#9443) * Add sbwf quilt * Fix tags * Update meta * Use modules repo files * Update glimpse2 imputation subworkflow (nf-core#9434) * Update glimpse2 sbwf * Update test * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add `BEAGLE5` imputation subworkflow (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> * 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 <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add minimac4 imputation subworkfllow (nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cutadapt (nf-core#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 (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (nf-core#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: vagkaratzas <vagelaros.gee@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

@mashehu

* fastq_shortreads_preprocess_qc init * skip all nf-test init * fastq_qc_stats subworkflow update (nf-core#9643) * fastq_qc_stats subworkflow update - renamed and testing for skip all inputs case * bracket push * empty skip all test working * meta init * seqera ai filled inputs and outputs of meta * stub added * sarscov2 - fastq - seqfu - seqkit - deacon - single_end nf-test added * prinseqplusplus added * clumpify added, cat_fastq added, nf-test added for missing tools * Update WHATSHAP/PHASE container, topic versions and task.cpus (nf-core#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 (nf-core#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 <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <32259775+vagkaratzas@users.noreply.github.com> * 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 <jfy133@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> * Update RGI modules to be Nextflow strict syntax compliant (nf-core#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 <24893913+SPPearce@users.noreply.github.com> * Make RGI modules syntax compliant --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Generate normalised matrix with `variancepartition/dream` (nf-core#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 (nf-core#9521) * Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests * Add ontologies to tcoffee/regressive and upp/align modules (nf-core#9484) * add ontologies to tcoffee regressive * add ontologies to upp align * Add module PBMARKDUP (nf-core#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 (nf-core#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 (nf-core#9469) * Add deepvariant optional html * update snapshot * Update modules/nf-core/deepvariant/rundeepvariant/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * trigger html generation * revert config change --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * utils_nfcore_pipeline: fix small lang server error (nf-core#9492) fix small lang server error * Fix hisat2/align to support large genome indices (.ht2l) (nf-core#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 <noreply@anthropic.com> * Update shinyngs modules to latest release (nf-core#9488) * Update semibin/singleeasybin environment (nf-core#9495) * add new ontology term to tcoffee align (nf-core#9497) * tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (nf-core#9489) * Sort file listing so "first" file is deterministic * Declare closure parameter per strict syntax Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * Sambamba depth add region bed input (nf-core#9498) * sambamba add region bed input * fix linting * fix linting * Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix fasta_index_methylseq and fastq_align_dedup workflows (nf-core#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 (nf-core#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 <mashehu@users.noreply.github.com> * Update test --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * meta.yml schema: add `containers` section, fix order and simplify (nf-core#9503) * fix order * add container section * simplify schema * require https for singluarity * update and add topics to snakemake module (nf-core#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 <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * fix sambamba depth stub version (nf-core#9509) * fix stub version * stray module * anota2seq: wrong variable name for batch assignment (nf-core#9511) rename variable * fix(anota2seq): add gene IDs and handle empty results (nf-core#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 <suhrig@users.noreply.github.com> * fix(decoupler): reorder imports and ensure environment variables are … (nf-core#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules * Add strdrop/build (nf-core#9512) Add strdrop build * chore(deps): update infrastructural dependencies * 🔧 update image and bioconda container for VueGen to latest version (nf-core#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 <mashehu@users.noreply.github.com> * Update container name Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Apply suggestion from @mashehu * Apply suggestion from @mashehu --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * qsv/cat: bump version (nf-core#9518) Bump qsv * Update haplogrep3 recipe to use topics (nf-core#9523) Co-authored-by: nf-core-bot <core@nf-co.re> * semibin/singleeasybin: bump version + migrate to topics (nf-core#9517) * Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * remove unused folder * rename * trimmomatic revisit * cutadapt revisit * trimgalore revisit * bbduk revisit * fastp revisit * adapterremoval revisit * leehom checkpoint (nf-core#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 (nf-core#9533) * new module clusty * patch links docs * fix prettier * remove non-mandatory input 'algorithm' * also patch stub input * Bump TRGT to 4.1.0 (nf-core#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 <mashehu@users.noreply.github.com> * remove duplicate versions --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix missing quotes (nf-core#9535) * Fix dream to show more than 10 results (nf-core#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 <18577080+atrigila@users.noreply.github.com> * rename to more appropriate fastq_preprocess_seqkit (nf-core#9537) * New module - TD2 (added modules for td2.longorfs & td2.predict) (nf-core#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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/predict/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/td2/longorfs/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * 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 <24893913+SPPearce@users.noreply.github.com> * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run (nf-core#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 (nf-core#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 <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/rseqc/splitbam/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Updated snapshot --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * remove topics from multiqc (nf-core#9530) * remove topics from multiqc * versions_multiqc -> versions * Apply suggestion from @nvnieuwk * fix meta.yml after merge * bump to MultiQC version 1.33 (nf-core#9538) * bump to 1.33 * update snapshots --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Add strdrop/call (nf-core#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 (nf-core#9541) 5.0.0 * Channel -> channel in some subwfs (nf-core#9542) Channel -> channel * Migrate cat/fastq to topic channel (nf-core#9543) * Migrate cat/fastq to topic channel * Remove out.versions in related subworkflows * Update snapshots (again) * Add module picard/collectvariantcallingmetrics (nf-core#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 <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * fix tabix/tabix stub (nf-core#9544) * fix tabix stub * bump max shards to 16 * Unify msa modules (nf-core#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 <kadomu@gmail.com> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Fix missing version from subworkflow snapshot (nf-core#9548) * New module: whatshap/phase (nf-core#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 <45968370+famosab@users.noreply.github.com> * 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 <45968370+famosab@users.noreply.github.com> * Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel (nf-core#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 (nf-core#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 nf-core#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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> * 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 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> * Add index and threads to trgt/merge (nf-core#9545) * Fix test path modification (nf-core#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 <louislenezet@gmaio.com> * Update xenium ranger modules and subworkflows (nf-core#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 <175728472+Copilot@users.noreply.github.com> * comment out config * fix: make prek happy * fix typo * remove test files --------- Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Version update: Modkit repair, callmods and bedmethyltobigwig (nf-core#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 <jin.khoo@campus.lmu.de> * Update `GLIMPSE` sbwf (nf-core#9524) * Update glimpse sbwf * Update test * Update filter operation * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/nf-core/vcf_impute_glimpse/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add quilt imputation subworkflow (nf-core#9443) * Add sbwf quilt * Fix tags * Update meta * Use modules repo files * Update glimpse2 imputation subworkflow (nf-core#9434) * Update glimpse2 sbwf * Update test * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/main.nf Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Update subworkflows/nf-core/bam_vcf_impute_glimpse2/tests/main.nf.test Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add deprecation * Change ifEmpty --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Add `BEAGLE5` imputation subworkflow (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> * 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 <louislenezet@gmaio.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add minimac4 imputation subworkfllow (nf-core#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 (nf-core#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 <noreply@anthropic.com> * Update cutadapt (nf-core#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 (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#9568) * Remove .view() * Remove unecessary tags * Update trimgalore (nf-core#9570) * testing solo trim-galore container, without adding extra cutadapt and pigz * Syntax updates and topic version for manta modules (nf-core#9556) * update manta germline * topics convertinversion * topics convertinversion * topics manta/somatic * topics manta/tumoronly * Syntax updates and topics of jasminesv (nf-core#9554) syntax updates and topics of jasminesv * Update `Modkit pileup` (nf-core#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 <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> * Standarize and alignment for all imputation and alignment modules (nf-core#9566) * Standarize and alignment * Fix glimpse2 sbwf test * Fix test * Add comment * Update snapshot --------- Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> * Update Infrastructural dependencies * Remove .view() (nf-core#9567) * Bump strdrop to 0.3.1 (nf-core#9565) * Remove unecessary tags (nf-core#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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * 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 <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_removeadapters_merge/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 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 <jfy133@gmail.com> * update snapshot --------- Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: vagkaratzas <vagelaros.gee@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * FASTQ_REMOVEADAPTERS_MERGE added * paired-end, adapterremoval test added * adapterremoval test * comment removed * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * adapter removal and merge params added to meta.yml * comment updated * fastq_complexity_filter added, nf-tests udpated, meta.yml updated * variable renames * dedupe flag for clumpify * check if deterministic output * updating non-deterministic snapshot * Update subworkflows/nf-core/fastq_shortreads_preprocess_qc/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * warning message added in subworkflow's description, regarding required process configurations * CAT_FASTQ logic update --------- Co-authored-by: EliottBo <112384714+eliottBo@users.noreply.github.com> Co-authored-by: Alejandra Escobar <ales@ebi.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Kateryna Nemesh <121881939+kornkv@users.noreply.github.com> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> Co-authored-by: Hanh Hoang <134130358+sainsachiko@users.noreply.github.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude <noreply@anthropic.com> Co-authored-by: Diego Alvarez S. <dialvarezs@gmail.com> Co-authored-by: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet <louislenezet@gmaio.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Sebastian Uhrig <suhrig@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Henry Webel <heweb@dtu.dk> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Sameesh Kher <khersameesh24@gmail.com> Co-authored-by: Luca Beltrame <lbeltrame@users.noreply.github.com> Co-authored-by: Rayan Hassaïne <r.hassaine@hartwigmedicalfoundation.nl> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com> Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: HD Yi <haidongyi@gmail.com> Co-authored-by: Dongze He <171858310+an-altosian@users.noreply.github.com> Co-authored-by: Dongze He <32473855+DongzeHE@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jinn <155078830+jkh00@users.noreply.github.com> Co-authored-by: ra25wog <jin.khoo@campus.lmu.de> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>

ra25wog added 6 commits December 11, 2025 11:36

update yaml

d838e25

update main.nf

350ff3d

modified test runs

3240588

update bedmethyltobigwig tests

fc76ab7

update main

cef040b

update snapshot

9416309

ra25wog and others added 3 commits December 11, 2025 14:10

fix linting

e7005fc

update snapshots

b95940c

Merge branch 'master' into modkit_pileup

bc06738

Merge branch 'master' into modkit_pileup

571c232

Joon-Klaps reviewed Dec 12, 2025

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ra25wog added 2 commits December 12, 2025 11:34

remove config

ee95270

update module_args

1e647ca

nf-core-bot and others added 4 commits December 12, 2025 10:50

[automated] Fix linting with Prettier

d50ec18

Merge branch 'master' into modkit_pileup

21a0176

changed name

7ef8955

update main

79d459e

Merge branch 'master' into modkit_pileup

ccaaaf3

Joon-Klaps approved these changes Dec 12, 2025

View reviewed changes

jkh00 added this pull request to the merge queue Dec 12, 2025

Merged via the queue into nf-core:master with commit f7ce6a8 Dec 12, 2025
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jkh00 deleted the modkit_pileup branch December 12, 2025 12:50

		@@ -64,38 +64,7 @@ nextflow_process {

		test("[bam, bai], [fasta, fai], bed") {

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jkh00 commented Dec 11, 2025 •

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