Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests #9521
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* add ontologies to tcoffee regressive * add ontologies to upp align
* 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 * Update docker image * Add test case with limma contrast string * Format changes and add test with shrinkage
* 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>
fix small lang server error
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>
…erministic (#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 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 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 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>
* 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 stub version * stray module
rename variable
- 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>
#9516) fix(decoupler): reorder imports and ensure environment variables are set before importing modules
Add strdrop build
…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>
Bump qsv
Co-authored-by: nf-core-bot <core@nf-co.re>
* Update semibin2 module * Update snapshot * Remove unneeded snapshot section --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* 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 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>
* 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 * 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 sbwf quilt * Fix tags * Update meta * Use modules repo files
* 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>
* 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 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
…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>
* 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
…ved cutadapt versions, since it is now ported to topics
* Remove .view() * Remove unecessary tags
* 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>
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Note for reviewers:
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| take: | ||
| reads // channel: [ val(meta), [ reads ] ] | ||
| skip_trimmomatic // boolean |
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You didn't leave any notes in the PR description, so I'm not sure. Is it your intention that folks would want to run multiple trimming methods, which is why you've avoided a simpler trimmer param or similar, as fastq_qc_trim_filter_setstrandedness does (for example)?
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Exactly, the idea is to select 1 or more adapter removal (and/or merge) tools. This subworkflow is going to be part of the mega fastq QC/preprocessing subworkflow described here.
Potentially, with pipeline chaining, this could one day become its own standalone pipeline that would be executed before all fastq short read pipelines.
| skip_cutadapt // boolean | ||
| skip_trimgalore // boolean | ||
| skip_bbduk // boolean | ||
| contaminants // channel: [ reads ] // fasta, adapters to remove |
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Would this benefit from metas? I think we normally require those these days (not all of the modules/ subworkflows have caught up)
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At this point in time, I just sourced the inputs in the format that they are being used by the included modules. Will update accordingly when and if the module inputs are updated at module side ;)
| fastp_save_trimmed_fail // boolean | ||
| save_merged // boolean | ||
| skip_adapterremoval // boolean | ||
| text_adapters // channel: [ txt ] // adapters to remove, in adapterremoval text format |
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Same, think this could do with a meta
pinin4fjords
approved these changes
Dec 16, 2025
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pinin4fjords
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I wonder a bit how it fits into the landscape of other trimming/ preprocessing workflows, but nothing particularly objectionable
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Thanks! I'll wait for @jfy133 for a final review pass and will then merge. |
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draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests