add missing channels for workflow outputs#10918
Merged
atrigila merged 2 commits intonf-core:masterfrom Mar 16, 2026
Merged
Conversation
matthdsm
approved these changes
Mar 16, 2026
ctuni
pushed a commit
to ctuni/modules
that referenced
this pull request
Mar 17, 2026
* add missing channels for workflow outputs * collect bcl2fastq undetermined
github-merge-queue bot
pushed a commit
that referenced
this pull request
Mar 30, 2026
* tested and linted disambiguate module * topic migration crispresso2 (#10827) * topic migration crispresso2 * topic migration crispresso2 * topic migration crispresso2 * topic migration crispresso2 * topic migration crispresso2 --------- Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> * add missing channels for workflow outputs (#10918) * add missing channels for workflow outputs * collect bcl2fastq undetermined * Hisat build springcleaning (#10686) * remove redundancy in mem opts for hisat2/build - remove conflicting 'process_high_memory' label - fix error on missing memory instead of defaulting to MAX_VALUE (remove redundant line 37, fold loud fail into script) * re-test module, passing * update hisat2 version, match container from seqera containers, remove unneeded samtools dependency * change versions in hisat2 align too * return singularity * add name as co author * add singularity docker 2 ways (build: just hisat2-2.2.2, align: hisat2-2.2.2 + samtools-1.23) * update snap * update snap * Abyss (#10647) * working on abyss module * abyss ready * fix linting * Update description for abyss_abysspe * Removing TODOs Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> * Removing TODOs Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> * output is now gzipped * Update modules/nf-core/abyss/abysspe/main.nf Co-authored-by: Fernando Duarte <123090819+FernandoDuarteF@users.noreply.github.com> * Update modules/nf-core/abyss/abysspe/tests/main.nf.test Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> * updating abyss tests * Update modules/nf-core/abyss/abysspe/meta.yml Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> * Clarify ontology references in meta.yml Added comments to ontology references for clarity. --------- Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> Co-authored-by: Fernando Duarte <123090819+FernandoDuarteF@users.noreply.github.com> * Migrate gfaffix version topics (#10905) * Migrate gfaffix version topics * Fix linting * fix typo * Fix reviews * stageAs FASTQC input files to avoid basename file collisions (#10924) * update module: duphold (#10822) * Update main.nf * Update meta.yml * Update main.nf.test * Update snaps * Add bio.tools ID * Update modules/nf-core/duphold/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Update meta.yml * Fix version * Update meta.yml * Update meta.yml --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * updated macs3 to 3.0.4 and added topic channel (#10926) * Updated macs3 to 3.0.4 and added topics channel * updated meta * Updated meta - contributor & topcis eval * fix formatting * fixed formatting with pre-commit hook * Update modules/nf-core/macs3/callpeak/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fixed meta --------- Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Add ViralConsensus module (#9655) * feat: Added ViralConsensus module * fix: update test snapshots for Docker compatibility * fix: task.ext to optional inputs * fix: update configuration of ext.args in tests * fix: simplify test asserts, though breaks linting * fix: add meta map to fasta input * fix: tests match and sed/head handling * chore: remove shell redirect * fix(purge_dups): re-add prefix to output file names (#10919) fix(purge_dups): not using prefix????????? * Add module for vcfexpress (#10409) * added module for vcfexpress * added suffix and fixed linting * removed TODO and fixed formatting * fixed testing * Update modules/nf-core/vcfexpress/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/vcfexpress/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * updated meta.yml * added creation of lua file in test * removed 'vcfexpress' from version number in topic * fixed formatting * Update modules/nf-core/vcfexpress/tests/main.nf.test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * feat(tximeta/tximport): add tag directive (#10927) feat(tximeta/tximport): add tag directive for process labeling Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * Add new module: saltshaker/classify (#10914) * add saltshaker classify module and tests * pin pip version * add saltshaker classify module and tests * pin pip version * update test with nf-core saltshaker/call * fix linting * add saltshaker classify module and tests * pin pip version * update test with nf-core saltshaker/call * fix linting * edits from review * update snaps and meta.yml * only make vcf in stub if vcf is in args * add no-vcf tests --------- Co-authored-by: Irene Duba <irene.duba@scilifelab.se> * feat: add topic version emission to quant-related modules (#10931) Convert custom/tx2gene, tximeta/tximport, and summarizedexperiment/summarizedexperiment to emit versions via topic channels, enabling automatic version collection in downstream subworkflows. Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * removed redundant assertions * Update modules/nf-core/disambiguate/tests/main.nf.test Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> * Update modules/nf-core/disambiguate/tests/main.nf.test Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> * Update modules/nf-core/disambiguate/main.nf Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * fixed meta.yml and test snap * added ontology format for the txt output --------- Co-authored-by: gmarenne <51478108+gmarenne@users.noreply.github.com> Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: Srishti Arya <94794172+srisarya@users.noreply.github.com> Co-authored-by: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Co-authored-by: Cameron Lloyd <lloyd@med.unideb.hu> Co-authored-by: Fernando Duarte <123090819+FernandoDuarteF@users.noreply.github.com> Co-authored-by: Alejandro Efraín Marín Peralta <67405824+EfraMP@users.noreply.github.com> Co-authored-by: Tatiana Gelaf Romer <tatiana.gelafromer@pfizer.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Kevin-Brockers <57921086+Kevin-Brockers@users.noreply.github.com> Co-authored-by: Lucas Patel <17998891+lucaspatel@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: sofiademmou <97464042+sofiademmou@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Co-authored-by: Irene Duba <75395041+ieduba@users.noreply.github.com> Co-authored-by: Irene Duba <irene.duba@scilifelab.se> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This is to fulfill nf-core/demultiplex#379