Add new component: gridss/assemble - #12382
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imsarath
marked this pull request as draft
July 17, 2026 09:41
mashehu
reviewed
Jul 24, 2026
| 'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }" | ||
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| input: | ||
| tuple val(meta), path(bams), path(bais), path(preprocess_dirs) |
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| tuple val(meta), path(bams), path(bais), path(preprocess_dirs) | |
| tuple val(meta), path(bam), path(bai), path(preprocess_dir) |
singular should be fine. use it also in the other instances
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Applied the suggestions, 👍
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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@nf-core-bot fix linting |
mashehu
approved these changes
Jul 24, 2026
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Jul 30, 2026
* Bump `fgumi/*` to 0.5.0
Update the conda pin and Wave containers to fgumi 0.5.0 and regenerate nf-test snapshots.
Three test fixes were needed for behaviour changes in 0.5.0:
- fgumi/correct: `--umis` no longer accepts a comma-delimited list (repeat
the flag instead), and all fixed UMIs must now be the same length, so the
two stray 8mers were dropped from the 7mer list the test data uses.
- fgumi/duplex: `--min-reads` values must be >= 1, so '1,1,0' becomes '1,1,1'.
- fgumi/merge: inputs must already be sorted in the requested merge order.
The tests fed coordinate-sorted BAMs, so they now ask for --order coordinate
rather than the default template-coordinate.
* bump riker to v0.4.0 (#12250)
bump riker
* Update to topic `methydackel/*` (#12248)
* Update to topic
* Update sbwf
* Update test
* feat: mako module (#12155)
* feat: mako module
* fix: remove empty identifier, add self as maintainer
* Update to topic `mobsuite/` (#12254)
Update to topic
* Update to topic `mirtrace` (#12253)
Update to topic
* riker/multi: add RNA support (#12255)
* riker/multi: add extra inputs/outputs
* riker: add support for rna; extra inputs
* update meta
* fix linting
* Update to topic `mirdeep2` (#12252)
* Update to topic
* Update sbwf
* Update to topic `midas` (#12251)
Update to topic
* Limit fix linting to changed files (#12221)
* fix linting only in changed files
# Conflicts:
# .github/workflows/fix-linting.yml
* run `prek run --all-files`
* update to prettier 3.9.3
* don't lint .conda-lock
* update leviosam2 snapshot
* run prettier again
* update snapshot
* Add `process_long` to cellbender/removebackground (#12258)
* Add process_long label to cellbender/removebackground.
CellBender remove-background runs can exceed typical medium job time
limits, so the module should inherit the long-running process label.
Generated by Composer
* Use assert process.success outside assertAll in cellbender tests.
Align removebackground module test assertions with the newer nf-core
pattern for clearer failures when a process does not complete.
Generated by Composer
* bump minimal python for ruff to 3.10 (#12259)
* bump minimal python for ruff to 3.10
* run prek
* Add meta maps to kallistobustools ref and count modules (#12256)
* Add meta maps to kallistobustools ref and count modules.
Propagate meta on fasta and gtf inputs in kallistobustools/ref, emit meta
on the index output, and accept meta-tagged index input in count.
Generated by Composer
* Use assert process.success outside assertAll in kallistobustools tests.
Align module test assertions with the newer nf-core pattern for clearer
failures when a process does not complete successfully.
Generated by Composer
* Address review feedback on kallistobustools ref and count modules.
Remove redundant file existence assertions from ref tests, simplify
version extraction, and align optional output declarations with current
module conventions.
Generated by Composer
* Update to topic `mtnucratio` (#12267)
Update to topic
* Swap trycycler to topic (#12266)
* Swap trycycler to topic
* Pin same python/setuptools versions
* Remove versions block from trgt and fix tests (#12268)
* Remove versions block from trgt and fix tests
* Use nft-bam and -vcf
* Add stub to the stub test
* Swap tsebra to topics (#12265)
* Swap transdecoder to topics (#12264)
* Swap topas to topic (#12263)
* Add gcta/makebksparse module (#11002)
* Add gcta/makebksparse module
* Use sanitized snapshots for gcta/makebksparse tests
* Preserve gcta/makebksparse metadata
---------
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Add plink/missing module (#12273)
PLINK 1.9 --missing wrapper: reports per-sample (.imiss) and
per-variant (.lmiss) missing genotype rates and writes a new
binary fileset. Includes real + stub tests using the public
plink_simulated fixture.
* add new module: aardvark/compare (#12260)
* add new module: aardvark/compare
* Update modules/nf-core/aardvark/compare/main.nf
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Update modules/nf-core/aardvark/compare/main.nf
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* apply changes after fix
* Update modules/nf-core/aardvark/compare/main.nf
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Update modules/nf-core/aardvark/compare/meta.yml
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Update modules/nf-core/aardvark/compare/meta.yml
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Update modules/nf-core/aardvark/compare/tests/main.nf.test
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* update snaps
* update label
---------
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Add plink2/pmerge module (#12281)
Merge a second PLINK 2 fileset into the first and write a new combined
PLINK 2 fileset (pgen/pvar/psam) using plink2 --pmerge.
Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com>
* Make output optional in goatools/findenrichment (#12288)
* Add meta maps to cellranger ref modules and downstream consumers (#12257)
* Add meta maps to cellranger ref modules and downstream consumers.
Propagate meta through cellranger/mkgtf and cellranger/mkref, update
cellranger/count and cellranger/multi to accept meta-tagged references,
and add an input/output filename collision check to cellranger/mkgtf.
Generated by Composer
* Use assert process.success outside assertAll in cellranger tests.
Align module test assertions with the newer nf-core pattern for clearer
failures when a process does not complete successfully.
Generated by Composer
* Address review feedback on cellranger module tests.
Simplify assertions with sanitizeOutput for simple outputs, use versions
topic snapshots with selective file checks for complex modules, and
configure mkgtf collision testing via params.module_prefix.
Generated by Composer
* Fix mkgtf test config for Nextflow 25.10.2.
Declare a default module_prefix param so ext.prefix is valid in CI,
where Nextflow 25.10.2 rejects undefined params in process config.
Generated by Composer
* Update to topic `multiseqdemux` (#12310)
Update to topic
* Bakta, add json file to emited output files (#12308)
* capture json file output
* add json output file
* Add Bakta JSON output, update stub outputs, and mimic isolated HOME dir
- Emit JSON annotation file
- Include JSON in stub outputs
- Create temporary HOME directory for process execution
* update snapshot to match new assertions in tests
---------
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* implemented readgroup addition in fastq_align_chromap, since chromap has no option to do it (#12283)
* implemented readgroup addition, since chromap has no option to do it
* fix linting errors
* set default to false
---------
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* chore(busco/{busco,download}): update containers and clean (#12272)
chore(busco/{busco,download}): update containers and busco clean
* Bump custom/gtffilter to Python 3.14.5 with Wave containers (#12325)
The module template uses Python 3.10+ type syntax (str | None) after the
ruff target-version bump, so the environment is updated to Python 3.14.5
and Wave containers are generated via nf-core modules containers create.
Generated by Composer
* RGI/BWT: add files to generate actual result (#12270)
* add files to generate actual result
* bump rgi version, add topic to snapshot
* pin kma
* wave container
* Update modules/nf-core/rgi/bwt/tests/main.nf.test
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* fix versions snap and syntax
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update to topic `nail` (#12324)
Update to topic
* Update to topic `mykrobe` (#12312)
Update to topic
* Update MALT large taxonomy data files location (#12327)
* Update Kaiju to also emit the downstream required nodes file
* Include names file as well
* Update documentation
* update all Kaiju modules to topics
* Remove debug thing from sourmash
* Reset KMCP files
* [automated] Fix code linting
* Replace s3 URI for MALT taxoonomy file
---------
Co-authored-by: nf-core-bot <core@nf-co.re>
* Add plink/bmerge module (#12277)
* Add plink/bmerge module
Merge a second PLINK binary fileset (bed/bim/fam) into a first one using
plink --bmerge, emitting a new combined binary fileset.
* Annotate plink/bmerge file ontologies
* Update to topic `mudskipper/` (#12309)
* Update to topic
* Update to topic
* Update input test file
* Update to topic `muscle` (#12311)
* Update to topic
* Update test
* new suppa/generateevents module (#12292)
* new suppa module
* fix typo
* skip md5 unstable output + update snapshot
* fix snapshots and update
* update meta
* Update modules/nf-core/suppa/generateevents/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* expand args and combine params
* separate ioe/ioi args
* apply suggested changes
* simplify stub
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Bump trimgalore to 2.3.0 (#12331)
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
* Add regenie/runl1 module (#11768)
* Add REGENIE splitl0 module
* Update REGENIE splitl0 metadata
* Use shared test params for REGENIE splitl0
* Add REGENIE runl0 module
* Update REGENIE runl0 metadata
* Use shared test params for REGENIE runl0
* Add REGENIE runl1 module
* Update REGENIE runl1 metadata
* Use shared test params for REGENIE runl1
* Scope REGENIE runl1 test prefix override
* Align REGENIE runl1 style with runl0
* Support apptainer container engine in REGENIE runl1
* Remove REGENIE runl1 test prefix override
* fix(regenie/runl1): update meta.yml containers to new lint format
Use linux/amd64 platform keys, scan_id, and add a conda containers
section so the module passes the updated nf-core lint rules on master
(the merge queue was rejecting the PR on containers_section_* checks).
* Add hipstr module (#12287)
* Add HipSTR module
* Remove tabix from module as hipstr enviroment dont have it
* Remove tabix from module as hipstr enviroment dont have it
* Change config
* Change config
* Args for 3rd test
* Allow for bam-files arg even if it will not work
* Fix typo
* Simplify optional output files usage
* New module `savana/to` (#11849)
* add savana/to
* update test scenarios - test data too small to run cna
* address review feedback
* update tests + related changes + bump version
* formatting
* add meta maps for inputs
* porting subworkflow Bam applybqsr to nf core modules (#12188)
* Added cram_qc_mosdepth_samtools subworkflow to nf core and added tests
* Added tests
* Added main.nf subworkflow
* Update subworkflows/nf-core/cram_qc_mosdepth_samtools/tests/main.nf.test
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update subworkflows/nf-core/cram_qc_mosdepth_samtools/tests/main.nf.test
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update subworkflows/nf-core/cram_qc_mosdepth_samtools/tests/main.nf.test
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update subworkflows/nf-core/cram_qc_mosdepth_samtools/tests/main.nf.test
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update subworkflows/nf-core/cram_qc_mosdepth_samtools/main.nf
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Apply suggestions from code review
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Removed _ from line 24 in main.nf
* corrected line 24 in main.nf
* changed subworkflow and added tests bam_applybqsr
* Added tests
* nf-tests changes
* test: use different interval files for multiple intervals test
* test: use dedicated interval files from test-datasets
* rebased my commits
* added bam with intervals test
* Update .vscode/settings.json
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update modules/nf-core/gatk4/applybqsr/main.nf
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update modules/nf-core/gatk4/applybqsr/main.nf
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Added nextflow config and tests
* lint
* [automated] Fix code linting
* WHY?
* WHY?
* meta.yml
* minor changes, removed warnings
* metayml
* fix linting
* fix linting
* changed tests for gatk4 module - bam and bam in cram out
* changed tests for gatk4 module - bam
* changed tests for gatk4 module
* changed tests for gatk4 module
* Apply suggestions from code review
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Apply suggestions from code review
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* changed tests for gatk4 module
* removed error line 81 from main.nf
* snapshots
* fix tests
* refactor and simplify
* tests
* used .combine
* tests passing
* code polish
* Apply suggestion from @maxulysse
* Added ontology
* samtools_args to config
* Update modules/nf-core/gatk4/applybqsr/meta.yml
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---------
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
* Add gcta/fastgwa module (#11000)
* Add gcta/fastgwa module
* Use sanitized snapshots for gcta/fastgwa tests
* Fix gcta fastgwa sparse GRM prefix
* Use standard fastgwa test config
* hide conda-lock diffs by default (#12330)
* feat(busco/plot): new module, deprecate busco/generateplot (#12336)
* feat(busco/plot): new module, deprecate busco/generateplot
* refactor(fasta_gfx_busco_plot): migrate to busco/plot module
* Update modules/nf-core/busco/plot/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* chore(busco/plot): check filename
* chore(busco/plot): fix meta
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* New module/fmh funcrofiler (#12326)
* First pass fmh-funpofiler module
* ran prettier
* changes version for conda
* runs prettier again
* sanitizes snapshot
---------
Co-authored-by: baichom1 <baichom1@mskcc.org>
* fix: fix riker/multi/meta.yml (#12339)
* bump htslib module (#12341)
* Add ldak/thinpredictors module (#12293)
* feat: add ldak/thinpredictors module
Primary module: ldak/thinpredictors. Bundled test-dependency modules: (none).
Ported and reorganised from the LDAK module family (nf-core naming, fixed
container/version/contract issues).
* fix(ldak/thinpredictors): address review — window params as val inputs, add ontologies, minimise test assertions
* Add PLINK ontologies to LDAK thinpredictors metadata
---------
Co-authored-by: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com>
* Add ldak/kvikstep1 module (#12343)
* feat: add ldak/kvikstep1 module
Primary module: ldak/kvikstep1. Bundled test-dependency modules: (none).
Ported and reorganised from the LDAK module family (nf-core naming, fixed
container/version/contract issues).
* Correct ldak/kvikstep1 file ontologies
* style(ldak/kvikstep1): remove leading blank line and trim redundant test assertions
* fix(ldak/kvikstep1): pass phenotype selector through ext args
* test(ldak/kvikstep1): cover binary output contract
* test(ldak/kvikstep1): add binary output snapshot
* add aardvark merge (#12334)
* add aardvark merge
* Apply suggestion from @georgiakes
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Update modules/nf-core/aardvark/merge/main.nf
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
---------
Co-authored-by: Georgia Kesisoglou <georgiakes@gmail.com>
* Bump bismark to 3.0.0 (#12344)
* Bump bismark to 3.0.0
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
* Fix CI failures on bismark 3.0.0 bump
Escape backslashes correctly for YAML in meta.yml eval docs (bare
\. is not a valid YAML escape in a double-quoted scalar, causing a
scanner error), and fix a pre-existing stub gzip syntax lint failure
in methylationextractor unrelated to the version bump.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
* new module: genometester4/glistmaker (#12345)
* Add new component: genometester4/glistmaker
* remove hardcode kmer
* Update to topic and template `nacho/*` (#12335)
* Convert to template nacho/normalize
* Fix test
* Update to template nacho/qc
* Fix linting
* Update environment.yml
* Use nf-core containers
* Update to topic `motus/*` (#12261)
* Update to topic
* Update test and conda env
* Update conda env
* Update conda env
* Update test
* Update test
---------
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* feat(vcontact3): add vcontact3/prepareddatabases module (#11738)
* feat(vcontact3): add prepareddatabases module
* Update nf-core/vcontact3/prepareddatabases/environment.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* docs(vcontact3): update keywords and input/output in meta.yml
* Update nf-core/vcontact3/prepareddatabases/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* docs(vcontact3): update keywords in meta.yml
* test(vcontact3): update nf-test snapshots for version changes
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update nf-core/vcontact3/prepareddatabases/environment.yml
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* Update nf-core/vcontact3/prepareddatabases/main.nf
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* Update nf-core/vcontact3/prepareddatabases/meta.yml
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
* fix(vcontact3): restore versions.yml in stub, fix meta.yml schema, correct module path, bump container to curl-fixed build
* chore(vcontact3): remove old prepareddatabases files from incorrect path
* fix(vcontact3): migrate versions.yml to topic-based emission, remove unnecessary singularity pullTimeout config
* chore: retrigger CI (transient plugin download 504)
* chore: retrigger CI (transient plugin download 504, attempt 2)
---------
Co-authored-by: Rilwan Lawal <lawal@frontend1.eve.ufz.de>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Jimit Patel <140850774+JP-Bro@users.noreply.github.com>
Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Co-authored-by: JP-Bro <jimitvit@gmail.com>
* Swap taxpasta to topic channels (#12285)
* 12306 adding request db module to the nf coregapseq (#12333)
* added request db module and changed other modules to share one db
* linter fix
* wiring request db output
* update telescope version to 1.0.4 (#12218)
* update telescope version
* adding singularity container
* singularity to https pattern
* updating version and containers (but not yet snapshot)
* Updating snapshot
---------
Co-authored-by: Hannah Jones <jonesh1@cn093.nemo.thecrick.org>
* Update Infrastructural dependencies
* Bump Samtools to v1.24 (#12340)
* bump htslib/samtools to v1.24
* bump samtools container
* Update snapshots - batch 1
* Update snapshots - batch 2
* Fix linting
* Update snapshots - batch 3
* subwf fixes
* [automated] Update gpu snapshot
* fix linting
* more subwf snapshots
* migrate poolsnp to topic
* bam2fq: gzip -> bgzip
* bam2fq: gzip -> bgzip
* fix linting
* add bgzip version
* fix linting
* [automated] Update gpu snapshot
* update conda too
* fix poolsnp versions
* code polish
* regenerate markdup test
* Update modules/nf-core/samtools/samples/environment.yml
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* typo
* Include xz
* update sexdeterrmine and bam_sort_stats_samtools
* sexdeterrmine
* fix leehom tests
* update snapshots for bam_dedup_stats_samtools_umitools
* fix bgzip stub usage
* typo
* refactor tests for more consistency
* code polish
* better assertions
* samtools/fasta
* poolsnp
* xz
* xz
* fix stubs
* fix stubs
* no join on empty channels
* gzip > bgzip
* Apply suggestions from code review
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
* Update modules/nf-core/poolsnp/main.nf
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update modules/nf-core/poolsnp/meta.yml
* Apply suggestion from @SPPearce
* Fix poolsnp linting
---------
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Added option to pass on custom arguments to rastair modules (#12349)
* Swap verifybamid to topic (#12262)
* Swap verifybamid to topic
* Swap to sanitizeOutput and add stub
* Add stub and test
* Remove config
* val not eval
* Add mm2plus/index (#12353)
* Add mm2plus/index
* review comments
* Update container for genmod modules to v.3.12.0 (#12354)
* update container for genmod to v.3.12.0
* update conda environment files
* Add mm2plus/align (#12352)
* Add mm2plus/align
* Update test names and sanitize outputs - from review comment
* Add ontologies - couldn't find one for PAF
* Add sarscov to test names
* Swap snpsift to topics
* Add new module: `caddsv/run` (#12189)
* add new module: caddsv/run
* config --> config_file in main.nf.test
* remove config in main.nf.test
* address review feedback
* env tag update
* bump to 2.0.1 and use `nf-core modules container create` to generate seqera containers for it.
* update version capture
* update version in snapshots
* update meta.ymls
* add comment for stub + simplify extension logic
---------
Co-authored-by: mashehu <mashehu3@gmail.com>
* Swap snippy to topic channels (#12355)
* Swap snippy to topic channels
* findAll versions
* Update snapshot
* Add rclone copy (#12337)
* Include Rclone_copy module
* Include Rclone_copy module nf test
* update nf tests
* update meta.yml file
* fix versions emit
* fix meta.yml
* fix versions emit
* fix meta yml
* Update modules/nf-core/rclone/copy/tests/main.nf.test
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update modules/nf-core/rclone/copy/tests/main.nf.test
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update modules/nf-core/rclone/copy/main.nf
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update modules/nf-core/rclone/copy/main.nf
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* fix: transfers/checkers ratio to be 1:2
* update snapshot
* fix: fix snapshot assertion
* update snapshot
* fix: transfer http paths handling inside the module
* update test
* fix: remove http param from config
---------
Co-authored-by: zxBIB <antonia.saracco.ext@boehringer-ingelheim.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* bismark: bump to 3.1.0 (#12356)
* bismark: bump to 3.1.0
Bump all seven bismark modules (align, coverage2cytosine, deduplicate,
genomepreparation, methylationextractor, report, summary) from 3.0.0 to 3.1.0.
Containers regenerated with the new `nf-core modules containers create`
(Seqera Containers via Wave: docker + singularity, linux/amd64 + linux/arm64),
adding per-arch conda-lock files and the meta.yml containers block.
nf-test snapshots still need regenerating on native Docker (bismark's alignment
fails under local amd64 emulation); flagged in the PR for CI/native regen.
* bismark: apply nextflow lint -format + bump snapshot versions
Address review feedback on #12356:
- Run `nextflow lint -format` on all 7 main.nf (canonical leading-operator
ternary — reverting a hand-reformat to the older operator-trailing style).
- Bump the versions.yml entries in the nf-test snapshots 3.0.0 -> 3.1.0
(bismark 3.1.0 is a byte-identical drop-in on the standard path, so outputs
are unchanged; only the reported version differs) — per @SPPearce's suggestion.
* bismark: revert main.nf to container-URL-only change (fix nf-test compile)
`nextflow lint -format` rewrote the scripts into new strict-syntax constructs
(e.g. `catch (e: Exception)`) that pass `nf-core lint` (new parser) but fail
nf-test's runtime compilation (classic parser, nextflow 25.10.2):
'Unexpected input' / 'Module compilation error'.
Reverted all 7 main.nf to the base and re-applied only the container URL bump
(3.0.0 -> 3.1.0 docker tag + singularity blob), keeping the existing
classic-compatible syntax that the merged modules use.
* updated test evaluation strategy - check for files and statistics, instead of getREADs using the nf-bam plugin to avoid linting conflicts. (#12348)
* updated test evaluation strategy - check for ReadsMD5, instead of reads directly to avoid merge marker conflicts during linting
* Changed bam() stringency, since conda CI tests were failing
* Clean up tests, removed redundancy
* Updated snapshot
* Added seeds for bam alignments
* Updated snapeshots
* test for HeaderMD5sums and statistics for bam files, the docker and conda GetReadMd5 resulted in unstable hashes between my local and the github CI tests
* Updated snapeshot
* conda and docker produce different hashes for getReadsMD5 or getHeaderMD5, fall back strategy -> Test if file exists and get just the alignment statistics for bam files
* Just test for file names
* Updated snapeshots
* Updated snapshot post samtools version dump
* Implemented review comments
* moved fasta reference in meta
* Add new component: gridss/preprocess (#11988)
* Add new component: gridss/preprocess
* fix: conda profile by removing md5 check for bam.csi output
* Apply suggestion from @beatrizsavinhas
Co-authored-by: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
* fix: removed checkmd5sums and updated snapshot with files listing
* applied suggestion from @LouisLeNezet
* fix: gridss/preprocess linting
* change: modified the bwa index symlinking based on gridss requirement and removed nextflow config from nf-test
* Update modules/nf-core/gridss/preprocess/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---------
Co-authored-by: Beatriz Vinhas <beatriz.sa.vinhas@gmail.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Swap vireo to topics (#12365)
* Swap taxonkit to topics (#12357)
* Swap svtyper to topics (#12284)
* Swap svtyper to topics
* Update environment
* Pin different setuptools version
* Tabs to spaces
* update medaka to version 2.2.2 (#12366)
* Simplify fastq align chromap logic (#12364)
* updated logic
* just added an empty line
* Updated snapshot
* Implemented review suggestion
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---------
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Remove unused ch_versions from subworkflows (#12370)
* Remove unused ch_versions from subworkflows
* Remove null versions from snap
* Swap vcftools to topic (#12367)
* Swap strelka to topic channels (#12290)
* Swap strelka to topic channels
* Update subworkflow and remove stray bracket
* Convert skani modules to topic channels (#12369)
- Converted skani/dist, skani/search, skani/sketch, and skani/triangle to topic channels
- Changed versions.yml output to versions_skani topic channel
- Updated meta.yml with topic channel output specification
- Updated test assertions to use sanitizeOutput(process.out)
- All tests pass on both docker and conda profiles
Generated by GitHub Copilot
* CHELAE_TRIM: simplify module logic (#12363)
* simplify module logic
* further simplification
* long names
* Trigger Build
* fix(tximeta/tximport): add jq dep as workaround for yq missing its jq runtime dep (#12362)
* fix(tximeta/tximport): add jq dep as workaround for yq missing jq runtime dep
* fix(tximeta/tximport): pin jq, rebuild multi-package container
Pin conda-forge::jq=1.8.2 without the inline explanation (root cause
and upstream link belong in the PR description, not the environment
file). Rebuild the Docker/Singularity images via Wave from the updated
environment.yml so -profile docker/singularity actually pick up the
fix, not just -profile conda.
* test(tximeta/tximport): update snapshot for rebuilt multi-package container
The Wave-built multi-package image (tximeta + jq) resolves a slightly
different dependency set than the old single-package biocontainer,
changing the output content hashes for the non-stub tests. Regenerated
via nf-test --update-snapshot --profile docker on an x86_64 VM.
* fix(tximeta/tximport): pin LC_COLLATE=C for reproducible gene-level row order
tximport::summarizeToGene() reorders gene-level rows via base R's
rowsum(reorder=TRUE), which sorts by the process locale's collation
order. This made output content (and therefore snapshot hashes)
depend on which execution profile's locale happened to be active,
independent of the earlier container/jq fix. Fixing LC_COLLATE in the
template makes row order reproducible across docker/conda/singularity
regardless of the container or host's default locale.
Also regenerates the downstream quant_tximport_summarizedexperiment
subworkflow snapshot, which depends on tximport's gene-level output
and was still holding pre-PR values.
---------
Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io>
* Deterministic collect() ordering in tximport and RSEM merge counts (#12377)
* fix: deterministic collect() ordering in tximport and RSEM merge counts
TXIMETA_TXIMPORT and CUSTOM_RSEMMERGECOUNTS each stage a multi-file input
built by collect()ing per-sample process outputs on a queue channel. Queue
channels emit in task-completion order, which is non-deterministic across
runs, so the staged input list order (and therefore the task hash) changed
run to run even when nothing else did, breaking -resume.
Both scripts already derive sample identity from the staged file/directory
names rather than input list position, so sorting the collected list by
name is a no-op on outputs and only stabilizes the cache key. Follow-on to
the same fix already applied to CUSTOM_TX2GENE's input in
quant_tximport_summarizedexperiment.
* Trim inline comments to essential reasoning
Detailed rationale belongs in the commit message / PR description, not
narrated at the call site.
* Update Parabricks modules to use Parabricks version 4.7 (#11217)
* feat: update modules to Parabricks version 4.7
* fix: setting default num gpus to 1 instead of null. helps with local execution.
* fix: increasing default memory for local execution
* test: update snapshots
* fix: update starfusion to gpu_highmem task (since it uses rnafq2bam)
* fix: move bqsr test args from nextflow.config to main.nf.test for readability
* Apply suggestion from @famosab
* chore: remove --low-memory flag from modules. not all module support this new feature, but every module that does has is updated.
* chore: lint starfusion
* fix: update subworkflow inputs
* fix: clean mutectcaller to only have one meta field. Move tumor_name and normal_name into val inputs.
* add nvidia container registry to `.nf-core.yml`
* fix: add oci singularity mode to fix mksquashfs issue on g4dn.2xlarge
* chore: cleaning up registry list
* fix: removing singularity force mode to test if mksquashfs bug fix works here
* chore: simplify comment and use _fai for unused variable
---------
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: mashehu <mashehu3@gmail.com>
* Improve rclone copy (#12375)
* fix: include mata id into log file name
* update snapshot
* fix: update meta.yml with new output name for log file
* fix: update meta.yml
---------
Co-authored-by: zxBIB <antonia.saracco.ext@boehringer-ingelheim.com>
* Add rclone check and checksum modules (#12346)
* add rclone check and checksum
* Update main.nf
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* change the order of inputs
* fix linting
* Update input for checksum and apply suggestions to sanitize output
* Modify input and update snapshots
---------
Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update last to 1652 (#12376)
* Update containers and environments to LAST 1652 and *tools 1.24.
* Add gzip to environments and containers.
* Refresh tests
* New module: Treerecs (#12371)
* initial commit for new treerecs module
* fix version and test
* add settings back
* with telemetry false
* Update .vscode/settings.json
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update modules/nf-core/treerecs/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---------
Co-authored-by: Lea Picard <lea-picard@deigo-login3.oist.jp>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Guard against running on an empty per-sample input list in tximport/quantify_rsem (#12378)
* Guard against running on an empty per-sample input list
toSortedList() always emits (even []) on an empty upstream, unlike the
collect() it replaced which emits nothing at all. Without a guard, that
turns a channel that previously never triggered its downstream process
into one that always does, running CUSTOM_RSEMMERGECOUNTS/TXIMETA_TXIMPORT
once with zero staged files whenever no samples reach this point (e.g.
all samples filtered out upstream). Filter to size() > 0 to restore the
original no-op-on-empty behaviour.
* Trim comments to state the invariant, not the narrative
* feat: add msisensorpro/baseline module; clarify pro -d dual semantics (#11190)
* feat: add msisensorpro/baseline module
Wraps `msisensor-pro baseline`, which builds a trained baseline
microsatellite file from a panel of normal samples. The resulting
baseline is consumed by `msisensorpro/pro -d` to enable the per-site
trained thresholds recommended by the msisensor-pro maintainers for
tumor-only MSI calling (xjtu-omics/msisensor-pro#77,
https://github.com/xjtu-omics/msisensor-pro/wiki/Best-Practices).
The configure file required by `msisensor-pro baseline -i` is built
internally from the staged `*_all` files so pipelines can feed the
output of `msisensorpro/pro` on each normal directly into this module
as a collected channel, without hand-writing a configure file that
references Nextflow work paths.
* docs(msisensorpro/pro): clarify that -d accepts a scan list or a baseline
`msisensor-pro pro -d` documents two supported invocations
(cpp/distribution.cpp `ProUsage()` L199-L206): mode 1 with a raw scan
list and a hard threshold set via `-i`, and mode 2 with a trained
baseline. The module's input description only hinted at mode 1 by
calling the file a "micro-satellite list". Expand the description to
cover both modes, point to the baseline workflow recommended by the
maintainers, and mention that the hard threshold is configurable via
`ext.args`.
No behavior change.
* Added support for Cleanifier tool: cleanifier/download, cleanifier/index and cleanifier/filter (#12360)
* added 3 new modules supporting Cleanifier tool
* applied suggestions and tried fixing snapshot instability
* corrected cleanifier/index nf-test versions testing
* some more refinements
* reverted echo changes in cleanifier filter stub test
* Split output of `suppa/generateevents` (#12383)
* new suppa module
* fix typo
* skip md5 unstable output + update snapshot
* fix snapshots and update
* update meta
* Update modules/nf-core/suppa/generateevents/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* expand args and combine params
* separate ioe/ioi args
* apply suggested changes
* simplify stub
* split output
* stub generates gtf
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* docs: fixed description of UCSC_gtftogenepred in its meta.yml file (#12379)
fix: fixed description of UCSC_gtftogenepred in meta.yml
* New module `suppa/psiperevents` (#12384)
* sync with master
* fix meta and tags
* fix test
* Fix symbolic link creation for fasta file (#12380)
* Fix symbolic link creation for fasta file
https://github.com/nf-core/methylseq/issues/608
* Fix syntax for symbolic link creation in main.nf for groovy parsing
* Update: pangolin modules (#12211)
* update to topics, update deps and containers
* linting; remove testing of version.yml from nf-test files
* fix meta file
* implement reviewer comments
* linting update
* linting
---------
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Add new module: `octopusv/plotcircos` (#12374)
* add new module: octopusv/plotcircos
* meta.yml update
* Update modules/nf-core/octopusv/plotcircos/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* review feedback - update tests
* update snapshot
* update tests 2.0
* remove the version line from test
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Add new module: `octopusv/svcf2bed` (#12388)
* add svcf2bed components
* update test
* review feedback
* New module `suppa/psiperisoform` (#12389)
* sync with master
* fix meta and tags
* fix test
* new module suppa/psiperisoform
* fix meta
* fix meta
* migrate sequencetools/pileupcaller to version topic (#12381)
* migrate to version topic
* Update nf-test and snapshots
* update test and snapshot. Thanks @mashehu
* Update Infrastructural dependencies
* Update actions/setup-python action to v7
* Fix kaiju taxmp input file pattern (#12391)
* Update Kaiju to also emit the downstream required nodes file
* Include names file as well
* Update documentation
* update all Kaiju modules to topics
* Remove debug thing from sourmash
* Reset KMCP files
* [automated] Fix code linting
* Improve pick up of database inputs
---------
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
* Update shinyngs modules to r-shinyngs 3.1.1 (#12390)
Bump shinyngs modules to r-shinyngs 3.1.1 with Seqera Containers metadata
Updates all 4 shinyngs modules (app, staticdifferential, staticexploratory,
validatefomcomponents) from r-shinyngs 2.4.0 to 3.1.1, using the new
nf-core/tools `modules containers create` command to build multi-arch Wave
containers and populate each module's meta.yml with containers:/conda-lock
metadata (matching the fastqc/multiqc precedent).
Also fixes the staticdifferential test's --unlog_foldchanges invocation:
it's a boolean store_true flag and must not be passed a value.
* Muse: Check age of index before touching (#12392)
* added new module: hackgap/count (#12386)
* added new module: hackgap/count
* tool parameter -o changed to --out for more clarity
* adjusted module cpu handling to be similar to tool
* updated to new snapshot
* removed cpu assignment for <4 task.cpus
* Pin nvcr.io/nvidia/tensorflow Docker tag to 9206ed8 (#12208)
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Methurator update (#12398)
* update container version
* remove compute_ci parameter
* update plot snapshot
* New module `suppa/psiperevent` (#12400)
* sync with master
* fix meta and tags
* fix test
* new module suppa/psiperisoform
* fix meta
* fix meta
* new module suppa/diffsplice
* update meta
* unstable files + update snapshot
* update including optional log tpm
* include tpm in snapshot
* check that method is valid
* test lower bound
* update snapshot
* add versions to snapshot
* Modify inputs in rclone check and checksum (#12394)
* Modify inputs in rclone check and checksum
* Fix linting and tests
* Use rclone's copy-links instead of copying input sumfile
* Capture exit codes
* Update meta
* Update tests
* Use sumfile for snpeff dir from test-datasets repo
* Update dependency nextflow-io/nextflow to v25.10.7 (#12210)
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Update shinyngs modules to r-shinyngs 3.2.0 (#12407)
Bump shinyngs modules to r-shinyngs 3.2.0
Updates all 4 shinyngs modules (app, staticdifferential, staticexploratory,
validatefomcomponents) from r-shinyngs 3.1.1 to 3.2.0, rebuilding the
multi-arch Wave containers and containers:/conda-lock metadata via
`nf-core modules containers create`.
The CLI additions in 3.2.0 (--pca_scale, and several --heatmap_* layout
options in make_app_from_files.R) are purely additive with existing
defaults, so no module or test changes were needed beyond the version bump.
* New module: ANGSD/SOAPSNPCALIBRATION (#12406)
* Add dedicated process for angsd soapSNP calibration step
* Update emit channel name to "soapsnp_calibration"
* Add tests for soapsnpcalibration process
* Add config for tests
* Add meta.yml for angsd/soapsnpcalibration
* Add comment to clairfy why -GL 3 and -minQ are hard coded
* Update main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update main.nf.test
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update main.nf.test
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update snapshot to reflect latest changes
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* topic channels migration phantompeakqualtools (#12408)
* topic channels migration phantompeakqualtools
* Updated testing strategy - to deal with unstable hashes
* Also report the versions in the snapshots
* pinned R version to match docker container
* New module `suppa/clusterevents` (#12410)
* sync with master
* fix meta and tags
* fix test
* new module suppa/psiperisoform
* fix meta
* fix meta
* new module suppa/diffsplice
* update meta
* unstable files + update snapshot
* update including optional log tpm
* include tpm in snapshot
* check that method is valid
* test lower bound
* update snapshot
* add versions to snapshot
* new module suppa/clusterevents
* fix environment.yml
* fix meta.yml
* fix meta.yml type
* fix the missing output and update snapshot
* bump default CPU and memory to use the full runner resources (#12402)
Co-authored-by: Felix Krueger <fkrueger@altoslabs.com>
* add:mgnifam_generatefamilies (#12409)
* add:mgnifam_generatefamilies
* Update modules/nf-core/mgnifam/generatefamilies/meta.yml
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update modules/nf-core/mgnifam/generatefamilies/meta.yml
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* test files from modules/ repo
* python versions align, added stub test as documentation-case for command available parameters to override
* quoting config process name
* fixing ext.args brackets to avoid test errors on the github runners
* init params module_args to empty
* Update modules/nf-core/mgnifam/generatefamilies/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* lint fix + less verbose comment for test + simplify versions out for mgnifam
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* feat: Add sentieon label to qualcal process (#12413)
Sentieon QualCal was missing it's label, probably a mistake.
* feat(shinyngs/app): add optional gene_sets and enrichment_results inputs (#12412)
* feat(shinyngs/app): add optional gene_sets and enrichment_results inputs
Add two optional path inputs so GSEA-style enrichment result tables and
gene-set GMT files can be baked into the shinyngs app object via the
existing shinyngs --enrichment_* CLI (shinyngs >= 3.1). Inputs are consumed
only through task.ext.args, so the script is unchanged. Existing tests pass
them as empty so outputs and the snapshot are unchanged.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* test(shinyngs/app): exercise gene_sets and enrichment_results inputs [skip ci]
Add a "mouse - with enrichment" nf-test case that stages the mh.all GMT and
per-contrast GSEA report tables and passes them via --enrichment_gene_sets /
--enrichment_filename_template, so the new optional inputs are actually
consumed by shinyngs at app-build time rather than passed as empty lists.
Fixtures are added in nf-core/test-datasets#2171; CI here must be re-run once
that merges.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* tmp: point modules_testdata_base_path at fork branch for enrichment fixtures
TEMPORARY: revert once nf-core/test-datasets#2171 merges to the modules branch.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* Restore modules_testdata_base_path to nf-core/test-datasets modules branch
Fixtures merged in nf-core/test-datasets#2171.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
* Update Parabricks modules to version 4.7.1 (#12404)
feat: bump version to Parabricks 4.7.1 and update snapshots
* Add module: sylph/query (#12399)
* First commit
* Accept changes in meta.yml
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Use full parameter name in script
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Use less repetitive input extension definition
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Merge branch 'master' into new_sylphquery
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* add:folddisco/index (#12418)
* add:folddisco/index
* up mem for github runners
* max mem up for gh runner, required by folddisco feature loaded feature space
* -y pdb hash algorithm to pass gh runner mem fail
* add:folddisco_query (#12419)
* add:folddisco_query
* Update modules/nf-core/folddisco/query/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* one config file
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Implement Jose's suggestion (#12423)
* update missing defs in main and conditional gzip outputs, meta yml missing fields (#12420)
* update missing defs in main and conditional gzip outputs, meta yml missing fields
* test names standardized and using sanitizeOutputs and unstable keys
* Update modules/nf-core/hmmer/hmmsearch/tests/main.nf.test
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* stray ; removed
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* full descriptive param names (#12424)
* Update EIGENSTRATDATABASETOOLS_EIGENSTRATSNPCOVERAGE (#12425)
* migrate to version topic
* Update nf-test and snapshots
* update test and snapshot. Thanks @mashehu
* always force json output
* Update nf-test and snapshot to remove now-obsolete test without json
* remove obsolete config clause
* Use long parameter names
* Bump shinyngs modules to r-shinyngs 3.2.1 (#12428)
Updates all 4 shinyngs modules (app, staticdifferential, staticexploratory,
validatefomcomponents) from r-shinyngs 3.2.0 to 3.2.1, rebuilding the
multi-arch Wave containers and containers:/conda-lock metadata.
r-shinyngs 3.2.1 is a patch release with no dependency changes, so no
module or test changes were needed beyond the version bump.
* Change arity for tumor-only mode: `nanomonsv/get` module (#12415)
* change arity for tumor-only mode
* change control arg
* Migrate ngmaster versions to topic channel (#12414)
* Migrate ngmaster versions to topic channel
* Update modules/nf-core/ngmaster/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Fix ngmaster version command
* Use compact ngmaster version extraction
* Fix ngmaster version metadata escaping
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Add new component: gridss/assemble (#12382)
* added gridss assemble module
* fix: input channels in nf-test and stub
* fix: nf-test gridss assemble
* update the nf-test snapshot
* fix: assemble main.nf-test
* fix: nf-core modules lint issue
* Update modules/nf-core/gridss/assemble/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update modules/nf-core/gridss/assemble/main.nf
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* applied suggestions
* fix: updated main.nf
* fix: nf-core modules linting
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update nf-core/setup-nextflow digest to 893c28b
* feat(prodigal): add condalocks (#12432)
chore(prodigal): add condalocks
* Updated iqtree to v3 and model output (#12430)
Updated modules and model output
* chore(prokka): update module including condalocks (#12431)
chore: update prokka module
* chore(pydamage): add conda locks (#12433)
* chore(pydamage): add conda locks
* refactor(pydamage): migrate versions to topic channel
Replace versions.yml output with an eval-based versions topic channel in
both pydamage/analyze and pydamage/filter. The NUMBA_CACHE_DIR and
MPLCONFIGDIR variables are set inline in the eval command since the
script-level exports are not visible to it.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
* refactor(pydamage): drop MPLCONFIGDIR from versions eval
Only NUMBA_CACHE_DIR is required: pydamage imports a module decorated with
@jit(cache=True), which fails when numba cannot write its cache next to the
read-only site-packages. MPLCONFIGDIR only silenced matplotlib/fontconfig
warnings on stderr, which the eval expression does not capture.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
* Migrate ngmerge to topic channels (#12442)
Generated by Codex
* fix(fastq_remove_rrna): drop redundant .first() on internally built SortMeRNA index (#12437)
* fix(fastq_remove_rrna): state value-channel contract on index inputs
ch_sortmerna_index and ch_bowtie2_index are paired with a per-sample
reads channel across multiple SORTMERNA and BOWTIE2_ALIGN calls, so
each must arrive as a value channel. A caller passing a single-item
queue channel instead would have it consumed once, silently limiting
the fan-out to one sample. State the constraint on both take: inputs
and in meta.yml.
Also drop the redundant .first() on SORTMERNA_INDEX.out.index: all of
SORTMERNA_INDEX's inputs are already value channels, so its output is
automatically a value channel and Nextflow flags the call as a
useless operator.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* revert: drop value-channel comments on unchanged inputs
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
* fix(gtf_hybridmerge_gffcompare): anchor withName selectors (#12435)
* fix(gtf_hybridmerge_gffcompare): anchor withName selectors
Nextflow matches withName as a full-string regex against the process's
fully qualified name. Written as GTF_HYBRIDMERGE_GFFCOMPARE:GAWK_FILTER
with no leading .*, the selector only matches when the subworkflow is
invoked directly at the top level. Inside a consumer pipeline the
qualified name is prefixed by the calling workflow chain and the
full-string match silently fails, so none of the ext.args/prefix/suffix
settings apply. For GAWK_FILTER this drops the -v codes_csv= argument,
producing an empty keep-set and no output, with no error raised.
Anchor all three selectors (GAWK_FILTER, BEDTOOLS_INTERSECT,
GAWK_CONCAT) with a leading .* so they match standalone and nested.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* revert: drop comment describing standard withName semantics
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
* Migrate nanolyse to topic channels (#12443)
* Migrate nanolyse to topic channels
Generated by Codex
* Use sanitizeOutput in nanolyse test
Generated by Codex
* fix(orftable_fasta_gtf_buildorfcatalogue): anchor withName selectors (#12434)
* fix(orftable_fasta_gtf_buildorfcatalogue): anchor withName selectors
`withName` is matched as a full-string regex against the fully qualified
process name, so `SUBWORKFLOW:PROCESS` selectors only apply when the
subworkflow is run standalone and never inside a consumer pipeline.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* fix(orftable_fasta_gtf_buildorfcatalogue): require value channels for references
`ch_fasta` and `ch_gtf` fan out against the per-sample ORF table channel.
A single-item queue channel is consumed by the first emission and the
remaining samples are silently dropped, so both must be value channels.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* revert: keep the defensive .first() on caller-supplied references
A comment in a take: block enforces nothing. Removing .first() from
ch_gtf and ch_fasta made a caller-supplied queue channel silently
process one sample and drop the rest, which is the failure this
component should tolerate rather than document.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* revert: drop comment on unchanged code
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* revert: drop comment describing standard withName semantics
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
Co-authored-by: Felix Krueger <fkrueger@altoslabs.com>
* fix(custom/orfnormalise): resolve PRICE gene ids from the annotation (#12436)
* fix(custom/orfnormalise): resolve PRICE gene ids from the annotation
PRICE's `Gene` column concatenates every gene overlapping an ORF's
genomic span with an underscore, so multi-gene ORFs were assigned ids
like `GENEA_GENEB`. Those are meaningless downstream and break joins
against single-gene count matrices.
Resolve `gene_id` from the GTF transcript-to-gene mapping first, and
only fall back to the `Gene` column when the transcript is absent from
the annotation.
Also anchor the `Id` parse on the row's `orf_type`. PRICE builds `Id`
as `<transcript_id>_<orf_type>_<n>`, and `split("_", 1)[0]` assumed the
transcript id contains no underscore, which holds for Ensembl but not
for all annotations.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* test(custom/orfnormalise): add snapshot for the PRICE gene-id test
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
* Migrate nextgenmap to topic channels (#12444)
Generated by Codex
* fix(ribotish/predict): pin python=3.13.9 to avoid Python 3.14 forkserver default (#12438)
* fix(ribotish/predict): ceiling python <3.14 in conda env
Ribo-TISH's predict.py stashes per-run state in module-level globals
set inside run() and reads them back in worker processes mapped
across a multiprocessing.Pool. That relies on CPython's fork start
method inheriting the parent's mutated globals. Python 3.14 changed
the default start method on non-macOS POSIX from fork to forkserver,
whose workers re-import the module fresh and never see those
globals, so ribotish predict -p >1 fails with
NameError: name 'genomefapath' is not defined.
Under -profile conda the environment could resolve a Python newer
than the container ships, exposing the bug for conda users while
container users were unaffected. Pin a ceiling rather than an exact
patch version so conda-forge can still supply patch updates within
3.13.x.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* fix(ribotish/predict): use exact python pin per environment schema
nf-core's environment-schema.json requires exact version pins
(rejects < and > operators), so pin conda-forge::python=3.13.9
rather than a range. 3.13.9 is the Python version already shipped in
the module's biocontainers image, so conda and container users now
resolve the same interpreter. Also reorders dependencies to match
nf-core lint's alphabetical sort.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* test(ribotish/predict): hash transprofile content in sorted order
ribotish maps per-transcript work across a multiprocessing Pool with
imap_unordered, so rows are emitted in arbitrary order and a plain md5
of the file cannot be reproduced between runs.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* test(ribotish/predict): snapshot transprofile by name
Row order comes from a multiprocessing Pool with imap_unordered, so a
content hash is not reproducible between runs.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* test(ribotish/predict): hash transprofile over sorted lines
Row order comes from a multiprocessing Pool using imap_unordered, so the
raw file md5 is not reproducible between runs while the content is.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
* [update] xeniumranger import segemtnation (#12421)
* update xeniumranger import segemtnation
* correct container registry
* changes to name and implmenet rec from matthias
* made a msitake
* update snap
* switching to smaller test data
* fix missing tag
* adding nextflow.config
* Apply suggestion from @mashehu
* limit cpu, memory and time and import config
---------
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: mashehu <mashehu3@gmail.com>
* Mobsuite typer (#11664)
* Update Kaiju to also emit the downstream required nodes file
* Include names file as well
* Update documentation
* update all Kaiju modules to topics
* Remove debug thing from sourmash
* Reset KMCP files
* [automated] Fix code linting
* Add mobsuite/typer
* Address comments from @KateSakharova and @mashehu
* Fix meta.yaml
---------
Co-authored-by: nf-core-bot <core@nf-co.re>
* Update StaphSCAN module (#12446)
* Update staphscan container version to 0.4.1
* Update staphscan version to 0.4.1
* Update test snapshot with new version and timestamp
* Missed prettier for meta.yml for importsegementation (#12448)
* Update cnaqc module (#12440)
* updating cnaqc module with new package version
* updating environment.yml
* re-enable prek not just skipping over all files (#12403)
* remove file specifc workaround and run prek again on all files (#12458)
* Add optional filter file as input in rclone/copy (#12455)
* Add optional filter file as input in rclone copy
* Initialise param
* bismark/align: intra-instance -p threading (replace --multicore fork model for Bowtie 2 + HISAT2) (#12385)
* bismark/align: intra-instance -p threading (Bowtie2 + HISAT2)
Replace the --multicore fork resource model with an intra-instance -p
divisor (-p = task.cpus / n_instances; n = 2 directional/pbat, 4
non-directional, 1 combined-index, 2 combined_index_parallel+non_dir)
for Bowtie 2 and HISAT2. minimap2/rammap keep the legacy --multicore
auto-compute unchanged.
Lower peak RAM (one index load per strand instance instead of M forks
each re-loading the index), fuller CPU use, and byte-identical Bowtie 2
output (-p N --reorder is thread-invariant). Emits -p only when
task.cpus/n >= 2, else omits it (faithful single-thread-per-instance).
Adds 4 nf-tests asserting -p is emitted (bowtie2 dir/non-dir, hisat2,
combined-index) via a dedicated cpus=8 config; existing tests unchanged
(cpus=2 emits no -p -> byte-identical, snapshots unchanged).
* test: cap bismark/align -p threading tests at 4 cpus (CI runner ceiling)
The -p-threading tests requested cpus=8 to force the divisor to emit -p,
but nf-core CI runners have 4 cpus and nextflow.enable.strict=true rejects
a request exceeding available cores (req 8 > avail 4) before the process
runs. Drop to cpus=4 (the runner ceiling): directional -> -p 2, HISAT2
directional -> -p 2, combined (n=1) -> -p 4. The non-directional case at
4/4=1 now asserts -p is OMITTED, exercising the omit-below-2 boundary.
Verified 9/9 nf-test pass on native amd64 with the 3.1.0 container.
* bismark/align: trim verbose comments in -p threading module
Presentation-only pass on the intra-instance -p threading change:
condense the aligner thread-model comment block and drop internal
plan jargon in the test config/assertions. No logic, test, or
snapshot changes.
* bismark/align: drop redundant nextflow_pthreads.config (global cpus now 4 via #12402)
Fold the genome-prep arg separation into the default test config; tests
inherit the global cpus=4, so the dedicated 4-cpu config is no longer needed.
* bismark/align: simplify --multicore memory guard (review suggestion)
* Update to topic `metaspace/*` (#12247)
* Update to topic
* Update test
* Update output
---------
Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update to topic `metamaps/*` (#12246)
* Update to topic
* [automated] Fix code linting
* Revert "[automated] Fix code linting"
This reverts commit 3d0d2247df1994f307b38e138b15744bcdf859da.
---------
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* fix(gedi): make the genome index self-contained and relocatable (#12451)
* fix(gedi/indexgenome): index from a FASTA copy inside the index directory
GEDI records the -s path in the .fi it writes: a bare relative name when the
FASTA is co-located with the .fi, an absolute path otherwise. Passing a staged
input at the task work directory root therefore recorded an absolute path to a
file outside the emitted index, which AWS Batch with Fusion never materialises,
so PRICE failed in PriceCodonInference with "Could not read sequence from file".
Indexing from a copy inside the index directory makes GEDI record a relative
name, so the reference resolves wherever the index is later read.
Co-authored-by: Felix Krueger <fkrueger@altoslabs.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* fix(gedi/price): point the .oml at the staged index before running PRICE
The .oml records absolute paths to its members, fixed when the index was built,
so an index read from anywhere other than the directory it was built in does not
resolve: PRICE fails at .oml load. Rewriting those paths onto the staged index
makes a relocated index usable, which is what lets a published index be reused
and lets PRICE survive a work directory that no longer holds the build.
The rewrite is written into the task directory rather than the staged index,
because writing through a staged directory lands back at the upstream task's
storage prefix under Fusion.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* test(gedi/price): assert orfs.tsv format and magnitude, not an exact row count
The number of ORFs PRICE calls is not reproducible across environments. A single
CI run gives 370 rows under docker, 374 under conda and 379 under singularity,
against a snapshot of 377, so no pinned value can pass every profile. The count
also tracks thread count: 379 at 1 thread, 377 at 2, 370 at 4, 381 at 8.
Within one machine, container engine and thread count it is stable, which is how
the pinned value passed when the module was added. Forcing determinism by
running single-threaded costs 20 minutes against 5 and still leaves the value
machine-dependent, so it is not a route for a module test.
Snapshot the output filenames and versions, and assert the orfs.tsv header
columns and a row count between 300 and 450. That still catches PRICE producing
nothing or something wildly wrong, without pinning a number that drifts.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
* Update modules/nf-core/gedi/price/tests/main.nf.test
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* Update modules/nf-core/gedi/price/main.nf
* Update modules/nf-core/gedi/indexgenome/main.nf
---------
Co-authored-by: Felix Krueger <fkrueger@altoslabs.com>
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
* New module: duckdb/table2parquet (#12461)
* Add duckdb/table2parquet module
Converts a delimited text table (CSV or TSV, gzipped or not) to Parquet,
using DuckDB's Python…
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As a part of the distributed computing GRIDSS subworkflow #4498 , I added this gridss/assemble module. This module wraps the assemble step, which performs genome-wide break-end assembly: it takes the per-sample preprocessed data (along with the input BAM/BAI files and reference genome) and assembles the reads supporting candidate structural variants into a single
.sv.assembly.bam. This assembly is the input required for the downstream variant-calling stepPR checklist
Closes #4502.
topic: versions- See version_topicslabelnf-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