New module: SAVANA/RUN#11649
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Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update scvi-tools version to 1.4.3 * update scvi-tools solo container Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * update scvi-tools solo hash Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * emit versions Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * emit versions Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * lint fix Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * use right hash Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * use right hash Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * use right hash Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * formatting Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * formatting Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * formatting Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> --------- Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
* update scar scvi-tools version Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * hash Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * hash Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> * set torch cache Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net> --------- Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
…ns (nf-core#11419) feat(maltextract): migrate to topic channel versions and add stub
…11448) feat(smoothxg): migrate to topic: versions, add stub block - Replace versions.yml with eval() topic: versions emission - Simplify version command to single sed expression - Add stub block for GFA output - Add stub test with sanitizeOutput, script tests assert GFA existence + versions only - Remove stale non-determinism comment - Regenerate meta.yml, remove legacy versions output
* feat(whamg): migrate to topic: versions, add stub block, sanitizeOutput assertions * Standardize version emission and restore EDAM comments * fix(whamg): rename emit to versions_whamg per nf-core convention - main.nf: emit: versions -> emit: versions_whamg - meta.yml: output key versions: -> versions_whamg: Local lint: 56/0. Local nf-test: 2/2 passed. * fix(whamg): use nft-vcf for VCF assertions; simplify version sed Addresses reviewer feedback: - Version extraction simplified from grep|sed to single sed - VCF assertions now use nft-vcf plugin (path().vcf.summary) - tbi excluded from snapshot (unstable across container runtimes) - Snapshot deleted for regeneration * fixing tbi process block
…rsions (nf-core#11410) feat(prinseqplusplus): migrate to eval() topic channel versions, add stub - Replace versions.yml / END_VERSIONS heredoc with eval() topic channel per @SPPearce review requesting eval string pattern - Version extracted via: prinseq++ --version | cut -f 2 -d ' ' - Remove END_VERSIONS from both SE and PE script blocks - Add stub block with gzipped empty FASTQ + touch log - Remove // meta map comments from tests - Add stub test with sanitizeOutput - Remove legacy versions output block from meta.yml Contributes to nf-core#4570
…dy present) (nf-core#11415) * Migrate haplocheck to topic channel versions (topic: versions) - Converted versions.yml output to topic channel (versions_haplocheck) - Fixed version eval: pipe head -1 | awk '{print $2}' to handle multi-line output - Removed END_VERSIONS heredoc from script and stub blocks - Updated tests: sanitizeOutput on both tests - Removed legacy versions output block from meta.yml Contributes to nf-core#4570 * fix(haplocheck): update meta.yml for topic channel versions via lint --fix
…f-core#11408) * Migrate shasta to topic channel versions and add stub block - Converted versions.yml output to topic channel (versions_shasta) - Removed END_VERSIONS heredoc from script block - Added stub block with compressed outputs (echo | gzip) and mkdir for results dir - Updated tests: deterministic content snapshots for main test, sanitizeOutput for stub - Removed legacy versions output block from meta.yml - Restored EDAM ontology comments Contributes to nf-core#4570 * fix(shasta): replace meta.model with task.ext.args2 to satisfy main_nf_meta_key lint rule * fix(shasta): add memory=8.GB to test config; update assertion to use versions_shasta; regenerate snap * fix(shasta): remove redundant named-key versions snapshot assertions per migration guide * fix(shasta): migrate meta.model to val input channel; simplify version sed Addresses reviewer feedback: - meta.model replaced with val(model) input channel per nf-core spec (non-file mandatory args SHOULD be value channels) - Version extraction simplified from head|cut to single sed - Removed args2 workaround; restored explicit --config flag - Removed model from meta map in tests
…re#11403) * Migrate ssuissero to topic channel versions and add stub block - Converted versions.yml output to topic channel (versions_ssuissero) Uses hardcoded version (1.0.1) as tool does not provide CLI versioning - Removed END_VERSIONS heredoc from script block - Added stub block with touch for .tsv output - Updated existing test to use sanitizeOutput(process.out) - Added stub test case - Restored EDAM ontology comment (# TSV) Contributes to nf-core#4570 * fix(ssuissero): use val() for hardcoded version per reviewer Applies reviewer code suggestions: - eval('echo 1.0.1') → val('1.0.1') - Updated meta.yml version entries from eval to val type
…re#11436) * Migrate kofamscan to topic versions and implement stub testing * fix(kofamscan): remove echo wrapper and restore EDAM comments * fix(kofamscan): hoist setup block to top-level scope per reviewer feedback
* feat(pairix): migrate to topic versions and stub * fix(pairix): align meta.yml with main.nf and simplify snapshot assertions * fix(pairix): fix broken version extraction and remove echo wrapper
* add quilt2 sbwf * publishDir not necessary for the unittest * add a line to explain that the regionout key will be used to store temporarily the region and therefore shouldn't be used in the meta map * QUILT2 uses topics for versions * Add a test with the optional bamnames input file to ensure it does work properly * Update subworkflows/nf-core/bam_impute_quilt2/tests/main.nf.test Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> * fix linting --------- Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* New modlue: finaletoolkit/delfi This uses FinaleToolkit to calculate the DELFI score (Cristiano et al., 2019). cf. nf-core#11365 * New module: finaletoolkit/delfi * Remove unwanted leftovers * Address review feedback * Add missing file * Address review questions * Fix syntax error * Update snapshot * Apply suggestions from code review
* Update to topics * Update tests * Fix meta * Apply suggestions from code review Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> * Apply suggestion from @LouisLeNezet --------- Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
* fix: sentieon gvcftyper accepts intervals * style: line breaks in sentieon gvcftyper driver call Per @SPPearce review on nf-core#11582 — match the multi-line format used in sentieon/haplotyper. * lint: rename meta1..meta4 to meta2..meta5 per nf-core convention * test: drop tautological regression test The test asserted variantsMD5 differs from the buggy md5, but the genome.bed used here covers all variants in test.genome.vcf.gz, so the BED is a no-op and the md5 is the same with or without --interval. Surfacing the bug would require a gVCF with variants outside the BED's coverage, which the test-datasets don't provide.
feat(islandpath): migrate to topic: versions, add stub block - Replace versions.yml with val() topic: versions emission - Place // WARN: comment above conda directive - Add stub block for gff and log outputs - Add stub test with sanitizeOutput assertions - Migrate script test to findAll versions pattern - Remove // meta map comments from test inputs - Regenerate meta.yml, remove legacy versions output
* Update to topics * Put back alignment * Update version * Update test
Update to topics
* feat: civicpy/annotate module * fix: reviewer comments * feat: allow users to pass a pre-existing cache file via path cache * fix: docker container, cache * fix: add htslib version to outputs
* feat(gedi): add gedi/indexgenome and gedi/price modules Adds two modules wrapping the GEDI / PRICE toolkit (`bioconda::gedi=1.0.6a`) for Ribo-seq translated-ORF discovery. PRICE (Erhard et al. 2018, doi:10.1038/nmeth.4631) calls translated ORFs from ribosome profiling data with near-cognate start codon detection. `gedi/indexgenome` wraps `gedi -e IndexGenome`, producing the `.oml` genome index directory consumed by PRICE. `gedi/price` wraps `bamlist2cit` + `gedi -e Price`, taking a cohort of Ribo-seq BAMs plus the genome index and emitting ORF predictions (`*.orfs.tsv` + `*.cit` + sidecars). One-shot across the cohort - PRICE is not per-sample. Both modules use Wave-built community containers from `bioconda::gedi=1.0.6a`. The bioconda recipe was merged 2026-05-16; using Wave directly for now. Source: nf-core/riboseq#174. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor(gedi/indexgenome): use ${prefix} for the index output directory Previously hard-coded the output directory as `price_index`. Switching to `${prefix}` (default `${meta.id}`, overridable via `task.ext.prefix`) lets callers control the directory name and matches the nf-core convention for publishable directory outputs. The default ${meta.id} keeps the directory keyed to the reference id, so when `gedi/price` opens `${index}/${meta2.id}.oml`, the lookup still resolves provided meta ids match (already the case in the test chain). Snapshot regenerated: the index directory name in the output snapshot changes from `price_index` to the test's `homo_sapiens_chr20` (its meta.id). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(gedi/price): add real test using minimised chr19+chr22 fixtures Replaces the stub-only PRICE test with an end-to-end test that runs PRICE on a minimal cohort of four Ribo-seq samples (chr19+chr22, protein-coding-only reference). The cohort produces 380 ORF calls; snapshot captures the orfs.tsv line count for stability validation. Fixtures published in nf-core/test-datasets PR nf-core#2061. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(gedi/indexgenome): update meta.yml output name after ${prefix} refactor The earlier `${prefix}` refactor (commit 0ca4c45) changed the index output declaration from `path("price_index")` to `path("${prefix}")`, but the meta.yml output entry still hard-coded `price_index` — causing CI lint to flag `correct_meta_outputs: Module meta.yml does not match main.nf`. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * style(gedi/indexgenome): collapse leftover alignment padding on index emit After the `${prefix}` refactor (commit 0ca4c45) the index output line was the only `tuple val(meta), path(...)` emit in the module, so the 52-space alignment padding it kept from when the path was `price_index` no longer aligns with anything. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(gedi): correct licence (GPL-3.0) and Gedi description in meta.yml Two cross-cutting fixes from review of nf-core#11693: - Licence was Apache-2.0 in both meta.yml files; the upstream repo erhard-lab/gedi is GPL-3.0. Corrected. - "GEDI (Gene Expression Data Integration)" was unverified — the upstream README/wiki/paper don't expand the acronym that way. Replaced with the upstream one-liner phrasing. PRICE meta.yml also adds the verified PRICE expansion (Probabilistic Inference of Codon Activities by an EM algorithm) from the GEDI wiki. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(gedi/price): point fixtures at nf-core/test-datasets@modules nf-core/test-datasets#2061 merged; fixtures now live on the modules branch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
update methurator with .fai index file
* New module mifaser/environment Co-authored-by: Nick Waters <nickp60@gmail.com> Co-authored-by: Mirae Baichoo <miraep8@gmail.com> * New module mifaser/main Co-authored-by: Nick Waters <nickp60@gmail.com> Co-authored-by: Mirae Baichoo <miraep8@gmail.com> * New module mifaser/meta Co-authored-by: Nick Waters <nickp60@gmail.com> Co-authored-by: Mirae Baichoo <miraep8@gmail.com> * New module mifaser/tests Co-authored-by: Nick Waters <nickp60@gmail.com> Co-authored-by: Mirae Baichoo <miraep8@gmail.com> * mifaser/mifaser: add test snapshot Co-authored-by: Nick Waters <nickp60@gmail.com> Co-authored-by: Mirae Baichoo <miraep8@gmail.com> * mifaser: switch to biocontainers 1.60, fix db path Use quay.io/biocontainers/mifaser:1.60--pyh106432d_0 instead of ghcr.io/vdblab/mifaser:1.64d. Prepend \$PWD to staged db path so mifaser 1.60 resolves --databasefolder as absolute path rather than relative to its Python package directory. Co-authored-by: Nick Waters <nickp60@gmail.com> * mifaser: correct path of test file * mifaser: fix Java syntax error * mifaser: update snapshot * mifaser: bump to 1.64, use each path(db) Update container and conda env to mifaser 1.64. Change db input from `path db` to `each path(db)` so the database is repeated for every incoming sample. Note: Singularity image at depot.galaxyproject.org for 1.64 may lag behind bioconda — Docker (quay.io) confirmed working. Co-authored-by: Carolin Schwitalla <carolin.schwitalla@qbic.uni-tuebingen.de> * mifaser: update snapshots * mifaser: undo 866234d Co-authored-by: Carolin Schwitalla <carolin.schwitalla@uni-tuebingen.de> * mifaser: formatting --------- Co-authored-by: Nick Waters <nickp60@gmail.com> Co-authored-by: Mirae Baichoo <miraep8@gmail.com> Co-authored-by: Carolin Schwitalla <carolin.schwitalla@qbic.uni-tuebingen.de> Co-authored-by: Carolin Schwitalla <carolin.schwitalla@uni-tuebingen.de>
…pgrade, bump version (nf-core#11242) * Add rundbcan synteny_pdf as optional, topic upgrade, bump version to 5.2.8 * Resync version updated numbers * Bump to latest version * Update rundbcan/easysubstrate snapshots for dbcan 5.2.9 * Move string check assertions --------- Co-authored-by: Xinpeng021001 <xzhang55@huskers.unl.edu>
…#11716) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Add new component: cnvkit/coverage * fix: update cnvkit version to 0.9.13 and add quay.io prefix * [automated] Fix code linting * Apply suggestion from @nvnieuwk Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * fixed comments from reviewer - remove blank lines and move comments to meta.yml --------- Co-authored-by: aaron-de-cock <aaron.de.cock@student.howest.be> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
* Add regenie/step1 module * Refine REGENIE step1 inputs and remove PR test config * Expand REGENIE step1 tests for explicit phenotype inputs * Use genotype metadata for REGENIE step1 log output * Use genotype metadata for REGENIE step1 tag and outputs * Fix REGENIE step1 stub gzip syntax * Split REGENIE step1 prediction outputs * Move REGENIE step1 phenotype selectors into tuples * Emit REGENIE step1 phenotype selectors * Update REGENIE step1 maintainer metadata * Use HTTPS Singularity container for REGENIE step1 * Allow ext.prefix in regenie step1 * Remove is_binary from regenie step1 * Remove pheno_col from regenie step1 * Update regenie step1 snapshots after removing pheno_col
…core#11722) Remove estimator-multiple-cpu from cellbender/removebackground
…hannel versions (nf-core#11696) * Update simpleaf to 0.24.1 with Seqera Wave container and topic-channel versions - Bump simpleaf 0.19.5 -> 0.24.1 (Wave container community.wave.seqera.io/library/simpleaf:0.24.1--41e05fd46d838d92). - Align environment.yml pins with the container: alevin-fry 0.14.0, piscem 0.20.0, simpleaf 0.24.1. Removed salmon (no longer a simpleaf dependency in 0.24.x). - Migrate versions output from versions.yml emit to topic-channel emits per the new nf-core convention (matches t1k/build pattern). Each tool emits (process, tool, version) into the shared `versions` topic. - Update piscem index file assertions in tests: piscem 0.20 replaced .sshash/.json with .ssi/.ssi.mphf/_ver.json. Stub blocks updated to match. - Inline `ALEVIN_FRY_HOME=.` in the simpleaf eval expression because the eval runs in a separate shell context from the script block. - meta.yml regenerated by `nf-core modules lint --fix`, removed leftover versions.yml stanza. All nf-tests pass (5/5 simpleaf/index, 2/2 simpleaf/quant). nf-core modules lint shows 0 failures. * Bump simpleaf to 0.25.0 in index + quant modules simpleaf 0.25.0 (Wave: community.wave.seqera.io/library/simpleaf:0.25.0--b9f96d8b71a01864) bundles alevin-fry 0.15.0 with two upstream fixes that surfaced during the multiplex-quant work: - alevin-fry: per-record sample index now maps correctly to manifest ordinal in multi-barcode collation (fixes COMBINE-lab/simpleaf#195 — sample_name column omission and resulting polars i64 inference crash). - simpleaf: multiplex-quant auto-downloads chemistries.json on first use (fixes COMBINE-lab/simpleaf#196 — no more "Run `simpleaf chemistry refresh` first" error). Neither fix changes behavior for the index/quant code paths these modules exercise, but bumping keeps all simpleaf modules on a single, current container generation.
* Simplify dream contrast handling * fix pre-commit * Use lme4 as source for nobars * Apply suggestion from @delfiterradas Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> * Update modules/nf-core/variancepartition/dream/templates/dream.R Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> * Update modules/nf-core/variancepartition/dream/templates/dream.R * Update modules/nf-core/variancepartition/dream/templates/dream.R * Update test snapshot * Update test snapshot * Migrate to topic channel * Fix linting error * Revert changes in snapshot Fix formatting issue by adding a newline at the end of the file. * Revert changes in snapshot --------- Co-authored-by: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
clean repo, and more strict syntax fixes
Update to topics
Update test
* Velocyto to topics * Fix tests and linting
* Migrate snpsift/split to topic channel versions Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Drive snpsift/split join mode via ext.args instead of non-standard meta.split key Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Use args.tokenize() for exact -j flag matching in snpsift/split Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Apply review suggestion: simplify snpsift version eval to a single sed Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
* bots initial attempt * removed unnecessary temp output dir, and renamed output files, added comment for bug workaround * flagged the bug in the comment * execfile on PATH for shim, instead of local user/ path * stricter version eval to pass GitHub runners warnings * updated and tested for multiple primers * Update modules/nf-core/primerprospector/analyzeprimers/main.nf Co-authored-by: Tim Rozday <timrozday@ebi.ac.uk> * Update modules/nf-core/primerprospector/analyzeprimers/main.nf Co-authored-by: Tim Rozday <timrozday@ebi.ac.uk> * prefix only used in stub --------- Co-authored-by: Tim Rozday <timrozday@ebi.ac.uk>
* Add octopusv/merge module * test-data path fix * fix versioning * add test data and update default merging logic * update merge flag * update tests * nextflow lint fixes + test update * Adress review feedback * minor change in meta.yml * Update modules/nf-core/octopusv/merge/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/octopusv/merge/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/octopusv/merge/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/octopusv/merge/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * minor changes to test * remove edam for bgzip, add note to strategy_flag (meta.yml) * bump version + add upset plot output --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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PR checklist
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda