Update cmaple #9580
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Update cmaple #9580
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sateeshperi
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Dec 17, 2025
georgiakes
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Dec 30, 2025
* adding uncompression functionality * new versions output syntax * meta.yml updated
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Jan 5, 2026
* 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>
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New versions output syntax.
Allowing gzipped inputs parsing.
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda