Test mergability #1
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…lows (nf-core#3) * Started adding nf-microbe functions, modules. subworkflows, and workflows * Removed objects for later additions, and started fixing bowtie2 subworkflow * Added FASTQ_BOWTIE2_FASTQ snapshot and updated CI * Updated subworkflow tests * Fix CI attempt #1 * Fixed function tests and linting * Fixed failing nf-tests
nf-core#5) * Updated tags and components * Moved functions into a subworkflow, added cleanworkdirs module, and removed igenomes code so it can be taken care of at pipeline level. * Fixed linting errors * Load functions together
* Added plass/penguin module, added rmEmptyFastAs function to utils_nfmicrobe_functions, and added fastq_readassembly_fasta subworkflow * Updated tests and snapshots * Removed spades_log from snapshot
* Added phables modules * Added assembly extension and removed read preprocessing workflow * Fixed meta.yml linting * Fixed linting and test errors round 1 * Removed TODO statement * Updated phables docker containers and fixed linting * Updated phables to try and make docker work * Fixed conda options
* Updated assembly extension and added virus identification * Updated genomad/endtoend snapshot
…e#18) * Add PREFIX to SPADES warnings log (nf-core#6615) * Update main.nf * Update main.nf.test.snap * Update actions/setup-java digest to 2dfa201 (nf-core#6617) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update GTDBTK/CLASSIFYWF: Fix bash failing if nothing to move in output directory (nf-core#6618) * Fix bash failing if nothing to move in output directory (which is a valid behaviour) * HarshilAlignmentTM * Fix fq/generate (nf-core#6610) Update snapshot, add stub * Fix `seqcluster` (nf-core#6616) * change test data with smrnaseq data and fix fastq capturing * point to nf-core repo * add pairhmm threads to haplotypecaller (nf-core#6620) * Nextclade vers bump (nf-core#6356) * Update environment.yml * Update main.nf Updated containers to 3.8.2 * Update meta.yml * Update main.nf * Create nf-test.config * Create main.nf.test nf-test module * Create main.nf.test.snap * Create nextflow.config * Update main.nf fixing biocontainer issue * Update meta.yml * nextclade version bump from 2.12 to 3.8.2 * Update meta.yml * Update test.yml regenerated test.yml * Update modules/nf-core/nextclade/datasetget/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/nextclade/run/main.nf Co-authored-by: Simon Pearce <[email protected]> * Delete tests/modules/nf-core/nextclade/run/test.yml deleted * Delete modules/nf-core/nextclade/run/tests/nextflow.config Deleting * Delete modules/nf-core/nextclade/run/nf-test.config * Delete modules/nf-core/nextclade/datasetget/tests/nextflow.config * Delete modules/nf-core/nextclade/datasetget/nf-test.config * Update main.nf.test * Update main.nf.test making tag adhere to guidelines * Update main.nf.test add params block [this mainly because I couldn't run the test locally without it) * Update main.nf.test.snap * Update main.nf.test * Update main.nf.test add stub * Update main.nf.test * Update tests/config/pytest_modules.yml Co-authored-by: Simon Pearce <[email protected]> * Update pytest_modules.yml * Delete tests/modules/nf-core/nextclade/datasetget/main.nf * Delete tests/modules/nf-core/nextclade/datasetget/test.yml * Delete tests/modules/nf-core/nextclade/run/main.nf * Update main.nf.test add stub to nextclade/datasetget test * Delete tests/modules/nf-core/nextclade/datasetget/nextflow.config * Update snapshot * Update meta.yml * Update main.nf.test updated main.nf.test * Update main.nf.test.snap * Add stubs and swap to only snapshoting part of the json * Update modules/nf-core/nextclade/datasetget/main.nf --------- Co-authored-by: shahirnm <[email protected]> Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: Matthias De Smet <[email protected]> Co-authored-by: Nur M Shahir <[email protected]> Co-authored-by: shahirnm <[email protected]>
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda