Update md5sum module to be able to take multiple files #3610

SPPearce · 2023-07-07T13:32:22Z

Update md5sum module to loop over multiple files when given them, for instance R1 and R2 of a fastq pair.
Someone with more linux-fu than me should probably check that it will work with files with spaces in their names etc.

I have made the branch off a previous PR apparently, rather than the main, which is why there are some spurious commits in the history.

…odules into ngscheckmate_workflow

muffato

Hi @SPPearce . I would suggest an alternative mode whereby there is a single .md5 file with the checksums of all input files.

SPPearce · 2024-06-27T14:54:58Z

Hi @SPPearce . I would suggest an alternative mode whereby there is a single .md5 file with the checksums of all input files.

As an optional mode controlled by a value input?

muffato · 2024-06-27T14:58:35Z

Hi @SPPearce . I would suggest an alternative mode whereby there is a single .md5 file with the checksums of all input files.

As an optional mode controlled by a value input?

I think that'd be the way to go given my understanding of the nf-core guidelines.

modules/nf-core/md5sum/main.nf

SPPearce · 2024-07-01T11:11:20Z

@mahesh-panchal, @muffato, I've incorporated Mahesh's code and the ability to generate a single file.

modules/nf-core/md5sum/main.nf

mahesh-panchal

So looks go to me, but I'll leave it up to you if you want to wait for someone elses input on whether the bash is ok.

modules/nf-core/md5sum/main.nf

Co-authored-by: Matthieu Muffato <[email protected]>

SPPearce · 2024-07-01T12:28:05Z

Thanks both!

@SPPearce

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This changes just adjust the module to the vep defaults to avoid the issue. * Updated html pattern in VEP to be more generic * bump MultiQC version (#5884) bump MQC * Bump shinyngs modules (#5881) * Bump shinyngs modules * Bump versions for snapshot * Update CONCOCT module(s): conda build bump, stub, and nf-test (#5869) * Version update, stub, nf-test for concoct/concoct * Bump version, add nf-test, stub to concoct/mergecutupclustering * nf-test, stub, and version conda build version bump for concoct/extrafastabins * Remove a superfluous config and specify a used one * Update modules/nf-core/concoct/extractfastabins/main.nf Co-authored-by: Simon Pearce <[email protected]> * Remove superfluous config file * Clean up code * Repair all stub tests that were empty --------- Co-authored-by: Simon Pearce <[email protected]> * `fasta_binning_concoct` subworkflow: do not fail on join (#5824) * fix: do not fail on mismatch for samples not binned with concoct * Migrate to pytest * Improved Harshil alignment --------- Co-authored-by: James A. Fellows Yates <[email protected]> * new module: datavzrd (#5883) * Generated structure for new module * Implemented module * Added semi-functional tests * Cleaned tests - test don't work yet * fix main, start nf-test * add new test data * fix linting * try to assert folders * fix tests * change output to prefix * change to prefix * update to prefix --------- Co-authored-by: vickylaram <[email protected]> * samtools/reheader: Fix bug causing output name to be incorrectly evaluated (#5887) Fix bug causing output name to be incorrectly evaluated * nf-test for snpsites (#5284) * nf-test for snpsites * remove old pytest * Delete modules/nf-core/snpsites/tests/nextflow.config * Update modules/nf-core/snpsites/tests/main.nf.test Co-authored-by: Joon Klaps <[email protected]> * Update assert Co-authored-by: Joon Klaps <[email protected]> * renamed test Co-authored-by: Joon Klaps <[email protected]> * reverted the input * updated input...again Co-authored-by: Joon Klaps <[email protected]> * fixed typo Co-authored-by: Joon Klaps <[email protected]> * Regenerate snapshot and fix linting --------- Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Added prefix to gunzip and while keeping the default name as `archive.toString() - '.gz'` (#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda * add dedicated output channel for trimmomatic stderr log (needed for multiqc) (#5501) * created new output channel capturing stderr of trimmomatic * updated output channel for trimmomatic * Add stub test and update snapshots * Add stub and update tests * Fix linting and add tee --------- Co-authored-by: John Palmer <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> * `ariba/getref` port to nf-test, add meta to tuple and stub (#5877) * port to nf-test, add meta to tuple and stub * modify meta and fix tags * change from each to tuple * Pass annotation files to last-dotplot (#5885) * Pass annotation files to last-dotplot The annotation of the target (plotted horizontally) genome is passed as a new channel. The annotation of the query (plotted vertically) genome is passed as a new component of the first channel. This is because this module typically loops on a list of alignments of various query genomes (from samplesheet) to a single target genome. The annotation files are called `annot_a` and `annot_b` because they are passed to the `-a` and `-b` arguments of `last-dotplot`. * Put arguments on separate lines. * Add meta map and reorder channels. * Test with dummy annotation files. Thanks @SPPearce for the hint. * Add meta to bowtie build (#3848) * Add meta to bowtie build * Swap fastq ngscheckmate tests * Swap to nf-test * Remove spurious changes to bowtie2 * Actually revert bowtie2 * Add the rest of bowtie2 * Again * Revert bowtie2 changes * Swap to meta.id as prefix * Swap bowtie align to nftest * Update tests * Use nft-bam * Update modules/nf-core/bowtie/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Swap to testdata path * Update modules/nf-core/ngscheckmate/patterngenerator/main.nf * Swap index finding to $ * Fix vafncm test * Update meta * Remove bam header md5sum * Update fastq test * Update paired bam test * Delete modules/nf-core/bowtie/align/tests/nextflow.config --------- Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * nf-test for pilon (#5293) * nf-test for pilon * linting for license * Add stub and extra test * Swap to testdata_base_path * Add missing END_VERSIONS and alignment * Add optional outputs to stub --------- Co-authored-by: Simon Pearce <[email protected]> * Bump phantompeakqualtools 1.2.2 (#5889) * Add stub section * Update yml * Add nf-test * Get rid of pytest * Make lint happy * Update tests * Update tests to make lint happy * update tests * Make lint happy * Using the same version as CI of nf-test locally might be a good idea * Use wave images * Make lint happy * Simplify tests --------- Co-authored-by: Simon Pearce <[email protected]> * Added variance filtering to custom/matrixfilter (#5358) * Added variant filtering to matrix filter * Corrected indentation * Simplified function in single conditional block * fixed line indentation * Fixed whitespace * Fixed logic * line wrapping change * added whitespace around comments * [automated] Fix linting with Prettier * remove trailing whitespace * Update matrixfilter.R * Remove whitespace --------- Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Update md5sum module to be able to take multiple files (#3610) * Fix version string spurious text in singularity tests * Add config for subworkflow * Update md5sum module to work with multiple files * linting * Fix stub * Add option to generate single file * Update modules/nf-core/md5sum/main.nf Co-authored-by: Matthieu Muffato <[email protected]> * Simplify versions processing --------- Co-authored-by: Matthieu Muffato <[email protected]> * Add share to find path (#5899) * build: Bump deepvariant to 1.6.1 (#5801) * build: Bump deepvariant to 1.6.1 * interim dir not allowed to be a dot in 1.6 * Update modules/nf-core/deepvariant/main.nf Co-authored-by: Maxime U Garcia <[email protected]> * hack: Hard code version google/deepvariant#830 --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * bump somalier/extract and somalier/relate version (#5894) * bump version * nf-test migratino * revert ancestry * fix linting * Update snap * fix unicode space --------- Co-authored-by: Simon Pearce <[email protected]> * Added evigene/tr2aacds (#5898) * Added evigene/tr2aacds * Sorted file list and added activation script * Fixed issues raised by feedback * correct president stub (#5904) * correct president stub * Large update to module * Update prefix and meta --------- Co-authored-by: Simon Pearce <[email protected]> * Fix EClint errors (#5907) Fix EClint * New module: nanoq (#5896) * Add the new module nanoq * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * define the output_format * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * update the stub run with gzip * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> * Foldseek: createdb and easysearch modules version bump + stub nf-tests added (#5906) * foldseek/createdb version bump, added stub nf-test * foldseek/easysearch version bump, stub nf-test added * test.snap for createdb added * sourmash/compare stub, nf-test, snapshot (#4665) * sourmash/compare stub, nf-test, snapshot * Add sort * Add a sort * Update snap * Try sort inside the module * Add meta to output and change formatting on test --------- Co-authored-by: Simon Pearce <[email protected]> * adding chewbbaca/createschema module (#4512) * adding chewbbaca/createschema module * updated for handling a mix of uncompressed and compressed files * update the formatting * update the formatting * updated module to emit meta * updated test.yml * update pytest * clean the meta.yml * clean the meta.yml * clean the meta.yml * replaced conda package with environment.yml file * py-test to nf-test migration * add stub and update tests, snapshot * updated stub * update stub test * update stub test * bump the version * update * updating container version * updated test snapshot * updated nf-test snapshot * added libmamba to environment file * Fix tests and linting * Update modules/nf-core/chewbbaca/createschema/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <[email protected]> --------- Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: Sateesh <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * stubs and test for rnaseq modules - part II (#5861) * add stubs for rsem * add stubs for rseqc * add stubs for subread/featurecounts * add stubs for trimgalore * add stubs for ucsc/bedclip * add stubs and more tests for umitools/extract * update snap * update snapshot for umitools/extract * fix umitools/extract tests * Apply suggestions from code review Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> * affy/justrma add stub, nf-test and snapshot (#4651) * affy/justrma add stub, nf-test and snapshot * Update snapshot and environment * Update snap * Update modules/nf-core/affy/justrma/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Swap test data file paths, fix config, update snaps and stub --------- Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> * Bump fgbio versions and swap to nftest (#5624) * Convert callduplex and callmolecular to nftest and update version * Convert zipperbams * Convert groupreadsbyumi * Convert sortbam and add stubs * Convert filterconsensusreads * Update snapshot * Update modules/nf-core/fgbio/callmolecularconsensusreads/main.nf * Add collision checks, swap test data paths * Fix conda version and linting * Apply suggestions from code review Co-authored-by: Nils Homer <[email protected]> * Update modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml Co-authored-by: Nils Homer <[email protected]> * Update duplex snap --------- Co-authored-by: Nils Homer <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Added pbtk/pbindex (#5901) * Added pbtk/pbindex * Removed prefix * Added agat/spfilterfeaturefromkilllist (#5771) * Added agat/spfilterfeaturefromkilllist * Added AGAT config * Included test with agat config * bump stranger to 0.9.1 (#5910) bump stranger * Update nft-bam to v0.3.0 (#5912) * Add stubs for rnaseq subworkflows - part I (#5911) * fix stub and add tests + single snapshot * add stub * fix stub * snapshot versions + better snap for stub * add versions to snapshot + add tests for stub * Add stub tests + single snapshot * Add stub tests + single snapshot * maxime sorted * Add stub tests + single snapshot * Add stub tests * Add stub tests + single snapshot * code polish + update snap * update snapshot using nft-bam * Add stubs for rnaseq subworkflows - part II (#5913) * Add stub tests + single snapshot * Add stub tests + single snapshot * fix stub and update tests for kallisto modules * Add stub tests + single snapshot * Add stub tests + single snapshot * bcftools isec input can be bcf or bcf.gz as well as vcf.gz (#5685) * bcftools isec input can be bcf or bcf.gz as well as vcf.gz * Add stub and stub test * Update tests * Update meta.yml * Add stub to name of stub test * Update meta * Update tests Changes: - exclude .tbi files from snapshot due to failing conda tests - update main.nf.test.snap - specificy path type of the output * Update tests again Changes: - include versions - sort file name list for consistent order - update snapshot --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Theresa Störiko <[email protected]> Co-authored-by: Theresa Störiko <[email protected]> * Add stubs for rnaseq subworkflows - part III (#5921) * do not snapshot input * do not snapshot input * Add stubs for rnaseq subworkflows - part IV (#5922) do not snapshot input with stub * mulled biocontainer for vardict-java and htslib (#5920) * vardict-java bgzip mulled container * update bioconda env * code polishing Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/vardictjava/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * args3 for bgzip * args3 * Update snap * removed whitespace --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Add same file clash check to bioawk (#5926) * Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 (#5893) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/upload-artifact digest to 0b2256b (#5927) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * dysgu==1.6.4_version update (#5928) * all_files_update * Update environment.yml * update_meta.yml * input==input_bam * update_snapshot * meta.yml,tags.yml update * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * update_author --------- Co-authored-by: Famke Bäuerle <[email protected]> * ADD argNorm module (#5905) * ADD argnorm module * ENH correct pattern for 'hamronized' input * ENH specify hamronization command in script * ENH don't pass 'hamronized' as val * Fixed trailing whitespace * "single_end" is not relevant in this module * alignment * "db_args" to avoid any confusion with the input channel * Added a test to check $tool is provided * Implemented the stub mode * Added a test for the missing database * Reordered the arguments to match the script --------- Co-authored-by: Matthieu Muffato <[email protected]> * Sentieon license server - testing (#5856) * test it out * ci: Add license_message script nf-core/sarek#1380 https://github.com/DonFreed/docker-actions-test?tab=readme-ov-file * test: Add tests for sentieon bwamem Because the pytest-workflow tests are taking so long * Add scratch from meeting * Clean up sentieon secrets * ci: Fix Nextflow secrets setup * fix(sentieon): Remove encryption key because it won't get used * fix # * ci: Fix when to setup secrets * feat: Add sentieon auth mech secret * chore(sentieon): Remove bwamem pytest-workflow tests * fix: Spike in with environment variables * fix: Add SENTIEON_AUTH_DATA in env file The reason for this is because when we require it in the module it fails. That doesn't make sense for normal Sentieon users. They don't care, this is more of a GitHub actions thing. * docs(sentieon): Make this a README * test: Add local testing setup * test: Remove publishDir * style: Remove sentieon/bwamem * fix: Change comments to prints for debugging and better reporting * fix: Add a quote? * chore: Remove unnecessary variable * debug: Print variables * Fix typo Co-authored-by: Anders Sune Pedersen <[email protected]> * chore: Clean up code * docs: Write up all the learnings from Sentieon * style: Run prettier * style: Add tags for nf-core lint * docs: Clean up notes Co-authored-by: maxulysse <[email protected]> * chore: Add @DonFreed as maintainer --------- Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Anders Sune Pedersen <[email protected]> Co-authored-by: maxulysse <[email protected]> * Fix Sentieon CI (#5934) * ci: Remove setting secrets in pytest-workflow * ci: Add a longer note about conditionals https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions#using-secrets-in-a-workflow Secrets cannot be directly referenced in if: conditionals. Instead, consider setting secrets as job-level environment variables, then referencing the environment variables to conditionally run steps in the job. For more information, see "Contexts" and jobs.<job_id>.steps[*].if. * ci: Check for secrets in env Because if this is coming from a fork it will fail * disable conda setup when not using a conda profile (#5935) * stubs and test for rnaseq modules - part III (#5925) * improve bbmap_split stub * update stub tests * improve stub * single snapshot * fix stub + add stub tests * fix stub + add stub tests * fix stub * restore tags * fix stub + better stub tests * fix snapshot * NARFMAP segfault (#4895) * test(narfmap): Add segfault test * fix(narfmap): Clean up log error * test(narfmap): Should segfault * chore(narfmap): Bump to 1.4.2 * test(narfmap): Mark test as passing bioinformaticsorphanage/NARFMAP#10 * style: Add extra tag for nf-core/lint * test: Update all the snapshot declarations * chore: Add a TODO for poddar's test * narfmap cleanup (#5937) * chore: Add Note about issue * test: Remove bam name Co-authored-by: maxulysse <[email protected]> --------- Co-authored-by: maxulysse <[email protected]> * Add CRAM/index support to NARFMAP (#5946) * feat: Add cram/index support to narfmap * chore: Remove singularity image comment * test: Update tests for CRAM * Update actions/setup-node digest to 1e60f62 (#5947) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix bcftools plugin split (#5942) * bump bclconvert (#5952) * bump bclconvert * fix snapshots * bump multiqc (#5950) * bump multiqc * update snapshot * chore: bump picard (#5948) * bump picard * fix hsmetrics test * fix markduplicates * fix extractfingerprints * fix addorreplacereadgroups * fix crosscheckfingerprints * Add prefix to output file for barrnap (#5919) * Add prefix to output file * Update barrnap to nf-test * Update tags.yml * Add missing bracket and run test * Correct format of license * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Review suggestions * Prettier * Update meta.yml * Update tests --------- Co-authored-by: Simon Pearce <[email protected]> * chore(deps): update actions/setup-python digest to 39cd149 (#5961) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * LAST alignment statistics for MultiQC (#5902) * last train modified to output multiqc * Report alignment length and percent similarity, for MultiQC. * Update snapshot file. * Document the new channels * Fix indentation * Update test results. * Give a longer suffix for better MultiQC search patterns. --------- Co-authored-by: Mohammed Mahdi <[email protected]> * Update lofreq somatic and callparallel (#5931) * update lofreq callparallel and somatic ssh * [automated] Fix linting with Prettier * suggestions * remove files tests * label lofreq somatic * Update modules/nf-core/lofreq/callparallel/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * port lofreq/callparallel to nf-test * Swap to nftest * update paths * add meta * Update main.nf * modify main * update paths * fix small errors * Update modules/nf-core/lofreq/somatic/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update main.nf.test.snap --------- Co-authored-by: AitorOP <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Francisco Martínez <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Update dupradar.r according to new MultiQC (>=v1.22) config values (#5943) Update dupradar.r according to new MultiQC config values. Co-authored-by: Matthias Zepper <[email protected]> * Update the module: nanoq (#5964) * update nanoq module * update nf-test * Update Glimpse2 phase (#5944) * Update Glimpse2 phase * Fix label * Update snapshot * Update modules/nf-core/glimpse2/phase/main.nf Co-authored-by: Maxime U Garcia <[email protected]> * Update meta.yml --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Update dupradar test snapshot (#5966) * Update dupradar test snapshot * Dummy commit to try and trigger nf-test in ci * Revert "Dummy commit to try and trigger nf-test in ci" This reverts commit 130f998. * stubs and test for rnaseq modules - part IV (#5939) * fix stubs and add stub tests * fix linting * fix some linting * fix linting * better comment * change container * update snapshots * improve untar stubs * update snapshots * update snapshots * update env * better * use seqera containers * quay.io * proper usage * update snapshots * keep ubuntu for now * update tests and snap * update test and snapshot * update test and snapshot * Add new input to multiqc module for use with --rename_samples (#5973) * Add new input to multiqc module for use with --rename_samples * Update tests * update meta.yml * Add provision for sample_names * port `gridss/gridss` to nf-test (#5933) * port * remove pytest files * fix meta * Update meta.yml * fix indentation * update test with bam plugin * fix indents, try other test * remove --assembly flag for now --------- Co-authored-by: Maxime U Garcia <[email protected]> * by remove the 2>&1 to avoid the warning message. (#5974) * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.2 (#5975) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Handle empty files (#5720) * fix: emit all fastqs, remove global log file * fix: remove rg parseing * fix(subworkflow/bcl_demultiplex): remove rg parsing, output empty fastqs, remove log file * test: update snaps * lint: traill\ing whitespace * feat: include read group parsing and empty file check in single closure * test: update snapshot * fix: lint final new line * fix: lint trailing whitespace * fix: add branch and emit empty fastq channel * tests: update snaps * lint: trailing whitespace * fix: filter bool and add test * test: update snaps * test: assert empty file exist * test: assert empty file exist * test: check file exists, update snap * Update test.yml * Update test.yml * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * lint: fix lint --------- Co-authored-by: [email protected] <--unset> Co-authored-by: Simon Pearce <[email protected]> * new module: custom_gtffilter (#5965) * Add basic gtffilter implementation * Add gtffilter stub * Add gtffilter meta map * Update gtffilter meta.yml * Fix gtffilter formatting * Add first gtffilter tests * Fix problems in gtffilter module defintion * Add gtffilter nf-test snapshot * Add support for gzipped inputs to gtffilter * Add gtffilter gzip stub * Update nf-test definition for gtffilter * Add meta2 to fasta input Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Add fasta meta map to gtffilter test definitions * Add gtffilter MIT license text --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Fix gtffilter output definition (#5977) * Added agat/spmergeannotations (#5772) * Added agat/spmergeannotations * Added tests with config * Rename preprocess rnaseq (#5959) * Edit content with subworkflow name * Rename subworkflow folder * Readd subworkflow with old name, with deprecation * remove rogue word * Appease eclint * Remove test suite for deprecated subworkflow * Using Seqera containers for Sentieon to avoid LD_LIBRARY errors (#5823) * Using seqera containers for sentieon * update containers for sentieon modules with quay.io registry --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Adam Talbot <[email protected]> Co-authored-by: maxulysse <[email protected]> * Swap unzip to nf-test (continuation of 5357) (#5897) * unzip stub, nf-test, snap * Revert "unzip stub, nf-test, snap" This reverts commit dec35aa. * Reapply "unzip stub, nf-test, snap" This reverts commit e0d708e. * added minimal required tests for process and stub * added snapshot * simplify snapshot input in stub test Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove unneeded stub files * migrate pytest for unzipfiles * add snapshot file for script block * added stub * added stub and stub test * updated stub snapshot for unzip * remove unneeded test config * Update snaps and malt * Update malt for linting * Fix linting for maltextract * Swap test-data paths for malt modules * Update modules/nf-core/maltextract/tests/main.nf.test --------- Co-authored-by: Sateesh <[email protected]> Co-authored-by: Jenny Leopoldina Smith <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Improve strandedness derivation in rnaseq preprocessing swf (#5982) * Improve strandedness devivation * Add missing params to nf-test * RNAseq preprocessing: rrna sequences make more sense as a channel of FASTAs, port tests (#5988) * rrna sequences make more sense as a channel of FASTAs * Also update tests * Add function test to swf * Fix up subworkflow function testing * [Upgrade] Normalize input of lofreq-viterbi to match other lofreq modules (#5989) * add meta2 to input fasta channel * update snapshot; nothing new but timestamp * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * Add module fgbio/collectduplexseqmetrics (#5960) * Initial commit * Rerun nf-test * Change assertion for duplex_qc output * Add ggplot2 to version.yml * Update snapshot * Correct conda packages version * Add Seqfu/derep (#5958) * add-usearch-unoise3 * add seqfu/derep * Delete modules/nf-core/usearch/unoise3/environment.yml * Delete modules/nf-core/usearch/unoise3/main.nf * remove files * update metadata * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/seqfu/derep/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Fix dataset in -stub * Clarify description * Update modules/nf-core/seqfu/derep/meta.yml Co-authored-by: Simon Pearce <[email protected]> * check for pre-existing output file && update test * Update main.nf --------- Co-authored-by: Simon Pearce <[email protected]> * modify valCutoff funtion in propr.R (#5995) Co-authored-by: Cristina Araiz <[email protected]> * liftoff: Re-added conda environment (#5981) * liftoff: Readded conda environment * Added liftoff to env file * Cleaned up env file * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.3 (#5996) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update: `CIRCULARMAPPER_CIRCULARGENERATOR` (#5997) * Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <[email protected]> * rename elongation factor for consistency with other CM module --------- Co-authored-by: James A. Fellows Yates <[email protected]> * Update: `CIRCULARMAPPER_REALIGNSAMFILE` (#5998) * Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * add meta to elongation factor channel for consistency with other CM module * update nf-test to include new meta * rename metas * Add stub and test to lofreq/indelqual (#5941) * Add stub and test to lofreq/indelqual * Add author * new test setup using --migrate-pytest and PR feedback * Update main.nf.test * Update meta.yml * Update main.nf * add snap; del pytest * Update meta.yml * Update main.nf.test * Update meta.yml * update test * minor fix in stub test * Update tabix and add threads (#5999) * Update tabix and add threads * fix linting * Remove problematic ifEmpty() from rnaseq preprocessing (#6000) * Refactor Sentieon (#5945) * refactor: Clean up the logic and let Sentieon figure it out * refactor: Remove Sentieon license server IP check * fix: Add a -n * Try accessing secrets in the module? * fix: Use Nextflow for if statement * update snapshot * update snapshot * extend logic to all main.nf * ci: Add Sentieon logic to pytest-workflow * test(sentieon): Add env section to every config * Revert "ci: Add Sentieon logic to pytest-workflow" This reverts commit 76884d2. * test: Remove pytest_modules for sentieon --------- Co-authored-by: maxulysse <[email protected]> * ltrharvest: Added test to verify graceful handling of no ltr input (#5978) * ltrharvest: Added test to verify graceful handling of no ltr input * Updated test data paths * Fixed test data path * Removed unstable items from snapshot * Updated snapshotting logic * ltrfinder: Added test to verify graceful handling of no ltr input (#5979) * ltrretriever/ltrretriever: Added test to verify graceful handling of … (#5980) * ltrretriever/ltrretriever: Added test to verify graceful handling of no ltr input * Removed unstable items from snapshot * update nf-test t0 0.9.0 (#6010) * Fix keyword meta (#6011) * Updated mkfastq module (#5984) * Updated mkfastq module * Combined input channels * Updated main.nf.test and snap --------- Co-authored-by: zxBIB Schcolnicov <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> * bulk update of meta.yml modules structure * update meta.yml files automatically with manual curation for missing information --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Carson J Miller <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Ramprasad Neethiraj <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Priyanka Surana <[email protected]> Co-authored-by: Matthieu Muffato <[email protected]> Co-authored-by: Aida Andrades Valtueña <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Usman Rashid <[email protected]> Co-authored-by: Anders Sune Pedersen <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Christian Heide <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Raquel Manzano <[email protected]> Co-authored-by: Matthias De Smet <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Maxime Borry <[email protected]> Co-authored-by: vickylaram <[email protected]> Co-authored-by: Tyler Chafin <[email protected]> Co-authored-by: Thanh Lee <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: John Palmer <[email protected]> Co-authored-by: John Palmer <[email protected]> Co-authored-by: Charles Plessy <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> Co-authored-by: thomgiles <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Matthieu Muffato <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: paulwolk <[email protected]> Co-authored-by: Lili Andersson-Li <[email protected]> Co-authored-by: Evangelos Karatzas <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Zohaib Anwar <[email protected]> Co-authored-by: Gisela Gabernet <[email protected]> Co-authored-by: Sateesh <[email protected]> Co-authored-by: Nils Homer <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: RuthEberhardt <[email protected]> Co-authored-by: Theresa Störiko <[email protected]> Co-authored-by: Theresa Störiko <[email protected]> Co-authored-by: eolaniru <[email protected]> Co-authored-by: poddarharsh15 <[email protected]> Co-authored-by: Vedanth Ramji <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: maxulysse <[email protected]> Co-authored-by: Sofia Stamouli <[email protected]> Co-authored-by: Mohammed Mahdi <[email protected]> Co-authored-by: AitorPeseta <[email protected]> Co-authored-by: AitorOP <[email protected]> Co-authored-by: Francisco Martínez <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Louis LE NEZET <[email protected]> Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: JIANHONG OU <[email protected]> Co-authored-by: Kyle Hazen <[email protected]> Co-authored-by: Nico Trummer <[email protected]> Co-authored-by: Adam Talbot <[email protected]> Co-authored-by: Jenny Leopoldina Smith <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: Thomas Krannich <[email protected]> Co-authored-by: Georgia Kesisoglou <[email protected]> Co-authored-by: Andrea Telatin <[email protected]> Co-authored-by: caraiz2001 <[email protected]> Co-authored-by: Cristina Araiz <[email protected]> Co-authored-by: Thiseas C. Lamnidis <[email protected]> Co-authored-by: Nicolás Schcolnicov <[email protected]> Co-authored-by: zxBIB Schcolnicov <[email protected]> Co-authored-by: Anabella Trigila <[email protected]>

* Conda remove defaults channel - structural changes (#5847) * Update `branch_update_staging` (#6657) * Added nf-test for seroba/run (#6372) * Added nf-test for sequenzautils/gcwiggle (#6373) * Added nf-test for sequenzautils/gcwiggle * Added stub and locked python version as per container * Added nf-test for segemehl/index (#6375) * Added nf-test for raven (#6378) * Added nf-test for scramble/clusteridentifier (#6376) * Added nf-test for pydamage/analyze (#6379) * Added nf-test for spring/compress (#6366) * Added nf-test for survivor/merge (#6364) * Added nf-test for gatk4/splitintervals (#6302) * Added nf-test for gatk4/splitintervals * Added stub test * Added nf-test for picard/scatterintervalsbyns (#6291) * Added nf-test for picard/scatterintervalsbyns * Added stub test * Update pre-commit hook python-jsonschema/check-jsonschema to v0.29.2 (#5938) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for pureclip (#6380) * Added nf-test for pureclip * Updated power assertion * Added nf-test for snippy/run (#6368) * Added nf-test for snippy/run * Explicitly tell snippy how much RAM we have * Only snap for vcf_csi * Actually update snapshot --------- Co-authored-by: Simon Pearce <[email protected]> * remove defaults from utils_nextflow_pipeline (again) (#6382) * Swap samtools collatefastq to nf-test (#5754) * Swap to nftest * Update output channels to not snap empty ones * Add too many stubs * Update stub definition * Add nf-test to metaphlan (#6139) * add nf-test to metaphlan * add config file * Remove metaphlan/metaphlan form pytest from config * Remove ypyest files * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * update nf-test * update snapshot for metaphlan subworkflow * update metaphaln/mergemetaphlan * Update metaphlan/metaphlan assertions * Add stub and fix tests * Update subworkflow * Try adding docker.runOptions * Actually commit the second config * Try adding no-same-owner * add config to docker * remove enable docker from config * Update snapshot --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * added trio options (#6164) * added trio options * added trio options * added trio options * added trio options * added trio options * added additional optional trio output * add addtional trio output in meta * remove pytest * removed redundant channles * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * some changes * corrected meta * removed environment.yml --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * New sections for further module info (#5876) new sections for further module info * Cafe (#6209) * First commit * Complete main.nf * meta.yml * First try test * Failed nf tests * working test * working tests * Make Prettier * fix * With snapshot * sn * fix doi * Add new emitted results and snapshot a result that does not have a time stamp or random model likelihood * Not working with cafe snapshot * Working tests * Add new output variables to meta.yml * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Add meta id (not working) * revert local files checks * back to s3 * Without channel of * Attempt to input data in test more verbose. Still not working * remove def * Fix version output in stub * With data on test-datasets * Fix test with variable pvalues, which was not reproducible * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Add paths to new modules location data * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Fix input test data paths --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for dshbio/exportsegments (#6398) * Added nf-test for dshbio/filtergff3 (#6399) * Added nf-test for bioawk (#6384) * Added nf-test for snpdists (#6417) * Added nf-test for slimfastq (#6418) * Added nf-test for snpsift/split (#6416) * Updated nf-test for strelka/germline (#6415) Updated nf-test for strelka/germline * Added nf-test for svtyper/svtyper (#6414) * Added nf-test for cdhit/cdhitest (#6388) * Added nf-test for emboss/cons (#6402) * Added nf-test for eido/validate (#6401) * Added nf-test for eido/validate * Fixed assertions * Added nf-test for vg/deconstruct (#6410) * Added nf-test for wgsim (#6409) * Added nf-test for gamma/gamma (#6408) * Added nf-test for ffq (#6407) * Added nf-test for vcflib/vcfbreakmulti (#6411) * Added nf-test for cnvkit/access (#6391) * Added nf-test for cooler/digest (#6395) * Added nf-test for clonalframeml (#6390) * Added nf-test for expansionhunterdenovo/profile (#6405) * Foldmason (#6355) * Add foldmason * Add test * fix prettier * fix prettier * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/foldmason/easymsa/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update main.nf * Update main.nf.test * Update meta.yml * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Add stub run tests --------- Co-authored-by: Simon Pearce <[email protected]> * Add tbi index as an output to lofreq callparallel (#6427) Add tbi as an output to lofreq callparallel Co-authored-by: fmartinez <[email protected]> * Update lofreq callparallel (#6429) * Add tbi as an output to lofreq callparallel * Update nf-test in lofreq callparallel * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update nf-test in lofreq callparallel * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update nf-test in lofreq callparallel --------- Co-authored-by: fmartinez <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * remove slashy strings from multiqc (#6431) * Added nf-test for cooler/makebins (#6396) * Added nf-test for seacr/callpeak (#6421) * Added nf-test for ectyper (#6400) * Added nf-test for shasum (#6419) * Fastqfilter (#6235) * First commit * Completed nf-test * Cleaned main.nf * Removed line in meta.yml * Modified meta.yml * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <[email protected]> * Added snapshot for lines in log test.log * made meta.yml prettier * Simplified version extraction --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for preseq/ccurve (#6423) * Added nf-test for emmtyper (#6403) * Added nf-test for cnvpytor/importreaddepth (#6394) * Added nf-test for cnvpytor/importreaddepth * Updated tool ver and snapshot * Locked numpy version * Added nf-test for cnvpytor/callcnvs (#6393) * Added nf-test for circexplorer2/annotate (#6389) * Added nf-test for plink/bcf (#6425) * Added nf-test for biobambam/bammerge (#6385) * Added nf-test for fasttree (#6406) * Added nf-test for fasttree * Update modules/nf-core/fasttree/meta.yml * Update modules/nf-core/fasttree/meta.yml --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for bwameth/index (#6387) * Added nf-test for bwameth/index * Updated tool ver and snapshot * Update modules/nf-core/bwameth/index/tests/main.nf.test --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for epang/place (#6404) * Added nf-test for epang/place * Fixed assertion * Added stub and updated power assertion * Added nf-test for biscuit/vcf2bed (#6434) * Added nf-test for sickle (#6440) * Added nf-test for peka (#6446) * Added nf-test for gfatools/gfa2fa (#6451) * Added nf-test for panaroo/run (#6450) * Added nf-test for plasmidfinder (#6444) * Added nf-test for gffcompare (#6452) * Added nf-test for elprep/split (#6459) * Update tests and fix compression (#6463) * Update tests and fix compression * fix * Added nf-test for tbprofiler/profile (#6437) * Added nf-test for varlociraptor/estimatealignmentproperties (#6436) * Deleted pytest of filtlong (#6456) Deleted pytest files for filtlong * Added nf-test for cnvkit/genemetrics (#6392) * Added nf-test for dshbio/splitgff3 (#6461) * Added nf-test for gappa/examineassign (#6455) * Added nf-test for gappa/examineheattree (#6453) * Added nf-test for stadeniolib/scramble (#6438) * Added nf-test for plink/vcf (#6443) * Added nf-test for sequenzautils/bam2seqz (#6441) * Added nf-test for sequenzautils/bam2seqz * Locked python version * Added nf-test for pmdtools/filter (#6424) * Added nf-test for pmdtools/filter * Added stub and conda version trap * Locked samtools * Added nf-test for pindel/pindel (#6445) * Added nf-test for pindel/pindel * Fixed linting issues * Added nf-test for vt/normalize (#6435) * Added nf-test for dshbio/filterbed (#6462) * Added nf-test for dshbio/filterbed * Fixed nf-test * Added nf-test for snpeff/download (#6439) * Added nf-test for snpeff/download * Fixed linting issues * Added nf-test for plasmidid (#6433) Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for entrezdirect/esummary (#6458) * Added nf-test for entrezdirect/esummary * Updated snapshot * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.3 (#6467) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Remove redundant rowname assignment (#6466) gene_info is derived from transcript_info, which only contains the columns "gene_id", "gene_name", but not "tx". Thus, the rownames assignment was not doing anything. Fortunately, the row names were not needed downstream regardless. * Update actions/setup-python digest to f677139 (#6471) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for scimap/mcmicro (#6442) * Added nf-test for scimap/mcmicro * Fixed typos * Removed module from nf-test/conda * Added nf-test for gfatools/stat (#6493) * Added nf-test for lissero (#6491) * Added nf-test for kleborate (#6492) * Added nf-test for qcat (#6422) * Added nf-test for qcat * Added stub and conda version trap * Added nf-test for maxbin2 (#6488) * Added nf-test for meningotype (#6487) * Added nf-test for methyldackel/mbias (#6485) * Added nf-test for mobsuite/recon (#6482) * Added nf-test for mobsuite/recon * Locked conda versions * Version bump * Added nf-test for purecn/normaldb (#6281) * Added nf-test for purecn/normaldb * Adjust environment * Add optparse * Try newer version from conda forge * Try adding r-utils too * Added wave containers, dynamic versioning and updated snapshot --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for msisensor2/scan (#6481) * Added nf-test for mykrobe/predict (#6479) * Added nf-test for mykrobe/predict * Fixed snapshot * Added nf-test for pasty (#6475) * Added nf-test for picard/collectinsertsizemetrics (#6473) * Added nf-test for nextgenmap (#6477) * Added nf-test for platypus (#6472) * Cleaned pytest files of porechop/abi (#6470) Cleaned pytest files for porechop/abi * Added nf-test for pbptyper (#6474) * Added nf-test for mash/dist (#6489) * Added nf-test for mtnucratio (#6480) * Added nf-test for nanolyse (#6478) * Added nf-test for nanolyse * Fixed snapshot * Added nf-test for paftools/sam2paf (#6476) * Added nf-test for snpsift/dbnsfp (#6469) * Added nf-test for eido/convert (#6460) * Added nf-test for eido/convert * Version bump and wave containers * Bump/wisecondorx (#6464) * bump wisecondorx to v1.2.9 * fix tests * Added nf-test for miniprot/index (#6483) * Added nf-test for fastawindows (#6457) * Added nf-test for fastawindows * Added stub and test * Added nf-test for gatk4/splitcram (#6303) * Added nf-test for hicap (#6495) * Added nf-test for vg/construct (#6468) * Added nf-test for paragraph/vcf2paragraph (#6448) * Added nf-test for paragraph/vcf2paragraph * Added version lock and trap --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for ngmaster (#6270) * Added nf-test for ngmaster * Added stub and version lock for python * Added nf-test for pbbam/pbmerge (#6447) * Added nf-test for pbbam/pbmerge * Updated modules, deprecation message and conda versions trap --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * Added nf-test for biscuit/index (#6386) * Added nf-test for biscuit/index * Added stub and updated snapshot * Added stub and nf-test for qc * Added stub and nf-test for pileup * Added stub and nf-test for epiread --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for macrel/contigs (#6490) * Added nf-test for macrel/contigs * Version bump and snapshot update * Added nf-test for metaphlan/makedb (#6486) * Added nf-test for metaphlan/makedb * Updated power assertion * Version bump and snapshot update --------- Co-authored-by: Lili Andersson-Li <[email protected]> * Added nf-test for lofreq/call (#6501) * Added nf-test for miranda (#6498) * Added nf-test for snapaligner/index (#6496) * Added nf-test for transdecoder/longorf (#6413) * Migrate renovate config (#6117) * chore(config): migrate config .github/renovate.json5 * Update .github/renovate.json5 Co-authored-by: Matthias Hörtenhuber <[email protected]> --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> * Added nf-test for mcroni (#6499) Co-authored-by: Famke Bäuerle <[email protected]> * Bump sniffles and add missing inputs/outputs (#6503) * Bump sniffles and add missing inputs/outputs * Update modules/nf-core/sniffles/main.nf Co-authored-by: Maxime U Garcia <[email protected]> * Update modules/nf-core/sniffles/meta.yml Co-authored-by: Maxime U Garcia <[email protected]> --------- Co-authored-by: Maxime U Garcia <[email protected]> * Added nf-test for vg/index (#6534) * Added nf-test for gvcftools/extractvariants (#6524) * No ".list" file is generated by this module (#6348) Co-authored-by: Famke Bäuerle <[email protected]> * remove "--outdir ." from fastq_screen bash command (#6247) * remove "--outdir ." from fastq_screen bash command fixes issue #6246 * adding optional fastqscreen output: fastq of nohits * fixing test.snap in fastqscreen module * fix linting fastqscreen/fastqscreen * Try pinning gdgraph, adding fastq test --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Added nf-test for dshbio/splitbed (#6516) * updated ensemblvep modules and added nf-tests (#6538) * updating ensemblvep modules * fix tests --------- Co-authored-by: Lucpen <[email protected]> * Add `mirTrace` module (#6507) * generate mirtrace module * fix linting * update tests and fix linting * update tests * update tests * Added nf-test for staphopiasccmec (#6535) * Added nf-test for ivar/trim (#6531) * Added nf-test for ivar/trim * Simplified version capture and added a trap * Version bump * Added nf-test for igv/js (#6529) * Added nf-test for icountmini/segment (#6528) * Added nf-test for hpsuissero (#6527) * Added nf-test for haplocheck (#6525) * Added nf-test for graphmap2/index (#6523) * Added nf-test for gappa/examinegraft (#6519) * Added nf-test for genmap/index (#6520) * Added nf-test for cnvkit/target (#6512) * Added nf-test for biobambam/bammarkduplicates2 (#6508) * Added nf-test for cooler/dump (#6514) * Added nf-test for cooler/dump * version bump * Added nf-test for goat/taxonsearch (#6522) * Added nf-test for goat/taxonsearch * Added suggested changes * Update actions/upload-artifact digest to 5076954 (#6540) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for getorganelle/config (#6521) * Added nf-test for calder2 (#6509) * Added nf-test for calder2 * Version bump * Added nf-test for mashtree (#6500) * Added nf-test for mashtree * Updated power assertions * Added nf-test for cellrangerarc/mkgtf (#6510) * Added nf-test for cellrangerarc/mkgtf * Excluded from conda profile * Added nf-test for cmseq/polymut (#6511) * Added nf-test for ismapper (#6530) * fix bug (#6541) * mcstaging/imc2mc (#6506) * create module * update meta.yml * add main.nf * add nextflow.config file * adding tests * finish tests * add conda exception in nf-test section of test.yml * change main.nf.test --------- Co-authored-by: Krešimir Beštak <[email protected]> * mcstaging/phenoimager2mc (#6143) * create initial module * added nextflow.config file * add test.snap * adapt main.nf to module * adapt meta.yml file * deleted env file * adapted nf.test * add test data specifications to test_data.config * added single files to test data * adapt input to file list, nor working yet * adapted to linting req, 3 warnings remain * successful tests, linting and prettier * ran test again for snapshot file * addressed minor comments in meta.yml * remove comment * remove conda test * adapt snapshot versions output and delete old snapshots * delete comment * add stub test * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <[email protected]> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <[email protected]> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <[email protected]> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <[email protected]> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <[email protected]> --------- Co-authored-by: Miguel A. Ibarra-Arellano <[email protected]> Co-authored-by: Krešimir Beštak <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Krešimir Beštak <[email protected]> * Add index output to bcftools reheader (#6542) * wgsim: add seed option, add stub, update test, match readsimulator pipeline (#6544) * add seed option, add stub, update test, match readsimulator * Apply suggestions from code review Co-authored-by: Felix Lenner <[email protected]> * change version assessment and hand seed via args * add versions md5 --------- Co-authored-by: Felix Lenner <[email protected]> * Added nf-test for estsfs (#6518) * Added nf-test for vrhyme/vrhyme (#6533) * Added nf-test for vrhyme/vrhyme * Locked dependency versions * Updated power assertions * Added nf-test for crumble (#6515) * Added nf-test for crumble * Now BAM is the default output format * Added nf-test for nanocomp (#6497) * Added nf-test for nanocomp * Updated power assertions * Fix gene table row naming in tximeta/tximport (#6551) Update tximport.r * Added nf-test for methyldackel/extract (#6549) * Added nf-test for methyldackel/extract * Version bump * Update motus/profile and add nf-test (#6212) * add nf-test to motus/profile * add stub runs to all tests * Update main.nf.test * Update main.nf.test.snap * Remove donwload db in stub run in main.nf.test * Try moving setups to just test (not stubs, as these don't need database download executed again) * update snapshot to fix conda nf-test instability --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> * Add tcoffee consensus module (#6539) * Add tcoffee consensus module * Add tcoffee consensus module * update snap * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Sateesh_Peri <[email protected]> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Sateesh_Peri <[email protected]> * Update main.nf.test * Update main.nf * Update main.nf * test * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf.test * Update modules/nf-core/tcoffee/consensus/main.nf Co-authored-by: Sateesh_Peri <[email protected]> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update tests * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * fix typos * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> * Add bcftools/plugintag2tag (#6547) Add bcftools/pluginstag2tag * Added nf-test for bwameth/align (#6550) * Added nf-test for bwameth/align * Update modules/nf-core/bwameth/align/tests/main.nf.test * update single-end test assert * print version yml * ignore syntax warning during version capture * Simplified the version extraction --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Sateesh <[email protected]> * Added nf-test for msisensorpro/scan (#6561) * nf-test + update to genotypegvcfs (#6553) * nf-test + update to genotypegvcfs * fix linting * review comments * fix old typo * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <[email protected]> --------- Co-authored-by: Felix Lenner <[email protected]> * Added nf-test for pirate (#6560) * Added nf-test for minia (#6564) * Added nf-test for purecn/intervalfile (#6558) * Added nf-test for haplogrep2/classify (#6572) * Added nf-test for hmmer/hmmfetch (#6574) * Added nf-test for mapdamage2 (#6578) * Added nf-test for biobambam/bamsormadup (#6579) * Fix wrong array definition in env schema (#6585) * new tool: jvarkit/vcfpolyx (#6580) * vcfpolyx, 1st commit * vcfpolyx * vcfployx, tests ok * fix env and meta ? * remove tab * remove ws * [automated] Fix linting with Prettier * fix conda ? * remove defaults * fix meta info * I hate myslef, fix warnings * add type to meta * fix snap md5 * fix meta3/meta4 https://github.com/nf-core/modules/pull/6580#discussion_r1745494016 * fix https://github.com/nf-core/modules/pull/6580#discussion_r1745463698 * Update modules/nf-core/jvarkit/vcfpolyx/main.nf Co-authored-by: Maxime U Garcia <[email protected]> --------- Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Sort bcftools merge inputs, add index output and nf-test conversion (#6586) * Sort inputs and nf-test conversion * update snapshot * update mirtrace (#6593) * Orthofinder (#6288) * working with orthofinder continue feature * Working resume test * With existing data from datasets and chose stable expected outputs. * updated snap shot (sorted) * fix test to have untar-ed workdir dir input * Fix folder direction * Add new output inputs to yml * fix tag * working conda on gitpod * force diamond install to 2.1.9 * Removed defaults --------- Co-authored-by: Usman Rashid <[email protected]> * Added nf-test for homer/annotatepeaks (#6573) * Added nf-test for homer/annotatepeaks * Removed defaults * Added nf-test for emboss/revseq (#6581) * Added nf-test for emboss/revseq * Removed defaults * Added nf-test for hapibd (#6575) * Added nf-test for hapibd * Removed defaults * Added nf-test for hypo (#6571) * Added nf-test for hypo * Removed defaults * Added nf-test for hmmer/hmmbuild (#6576) * Added nf-test for hmmer/hmmbuild * Removed defaults * Added nf-test for legsta (#6566) * Added nf-test for legsta * Removed defaults * Added nf-test for cnvkit/call (#6582) * Added nf-test for cnvkit/call * Removed defaults * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.4 (#6592) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for gubbins (#6598) * Added nf-test for gubbins * Version bump * Updated test names * Added nf-test for goleft/indexsplit (#6595) * Added nf-test for graphtyper/vcfconcatenate (#6596) * Added nf-test for geoquery/getgeo (#6594) * Added nf-test for geoquery/getgeo * Version bump and stub * Added versions trap * Locked r-base version * Updated power assertions * Fix bcftools merge for one sample (#6591) * Added nf-test for ivar/consensus (#6568) * Added nf-test for ivar/consensus * Verion bump * Added nf-test for circexplorer2/parse (#6577) * Added nf-test for circexplorer2/parse * Updated power assertion * Added nf-test for mmseqs/databases (#6563) * Added nf-test for mmseqs/databases * Updated power assertion * Removed defaults * Now sorting list * Bgzip and tabix paraphase (#6543) * Bgzip and tabix paraphase * Fixed snapshot size and added threads * remove defaults channel * fix tests * Added nf-test for ivar/variants (#6567) * Added nf-test for ivar/variants * Simplified version extraction * Version bump --------- Co-authored-by: Joon Klaps <[email protected]> * Added nf-test for gfaffix (#6597) * Added nf-test for gfaffix * Version bump * Fixed linting * Fixed versions * version fix * Added nf-test for idr (#6570) * Added nf-test for idr * removed defaults * Added nf-test for gunc/downloaddb (#6599) * Added nf-test for metabat2/jgisummarizebamcontigdepths (#6565) * Added nf-test for metabat2/jgisummarizebamcontigdepths * Removed defaults * Added nf-test for krona/ktupdatetaxonomy (#6569) * Added nf-test for krona/ktupdatetaxonomy * Removed defaults * Updated power assertion * Mega conda environment update: Remove `name` and `defaults` (#6600) * Remove defaults channel from all modules * Remove 'name' from conda environment files * Update conda environment schema * Remove defaults from env template and GHA CI * Update Prettier in GHA test.yml workflow to match pre-commit version * Remove whitespace from environment.yml files * hmmsearch, rank and output fasta (#6601) * New subworkflow fasta_hmmsearch_rank_fastas * Add euk and mito SSU rRNA to tests * More tests * Fix trailing whitespace * Pre commit all files (#6604) * GitHub Actions: Always run pre-commit with all files. * First attempt at pre-commit on all files, automatic fixes * Ruff lint: DecryptionTimeout -> DecryptionTimeoutError * Ruff: disable block in template that uses Nextflow variables * Module meta.yml licenses - arrays in strings should not be in strings * License arrays: formatting * Add keywords to module meta files that were too short * Misc module meta.yml fixes * Wrap string licenses as arrays * Type: string instead of value * Fix more meta types * More types, keywords * Apply suggestions from code review Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Boolean flag types --------- Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Added nf-test for elprep/filter (#6517) * Added nf-test for elprep/filter * Updated power assertion * Now emitting logs --------- Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for blat (#6603) Co-authored-by: Simon Pearce <[email protected]> * Added nf-test for quast (#6554) * Added nf-test for quast * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Tests for each optional input and removed pytest * Removed "ref, nogff" test --------- Co-authored-by: Famke Bäuerle <[email protected]> * bcftools csq (#6605) * bcftools csq * fix lint / format * env.yml * move fun at bottom * Update modules/nf-core/bcftools/csq/main.nf Co-authored-by: Sateesh_Peri <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]> * Add module and subworkflow mirtop (#6587) * add mirtop gff module * add mirtop/counts module * add mirtop/export module * add mirtop/stats module * update yml * add bam_stats_mirna_mirtop subworkflow * add required dependencies * update test * update subworkflow test * update yml and output files * fix tag linting issue? * fix linting * run prettier * try to solve conda issue * add a compatible pandas * fix linting * update failing ci mirtop/gff test * Added nf-test for angsd/contamination (#6602) * Added nf-test for angsd/contamination * Swap container version * Update snapshot --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Phil Ewels <[email protected]> * Add support for pip dependencies and force version pinning in conda (#6588) * Add support for pip dependencies and force version pinning in conda * [automated] Fix linting with Prettier --------- Co-authored-by: nf-core-bot <[email protected]> * Add `seqcluster` module (#6614) * add seqcluster module * run prettier * Update modules/nf-core/seqcluster/collapse/environment.yml Co-authored-by: Sateesh_Peri <[email protected]> * Update modules/nf-core/seqcluster/collapse/main.nf Co-authored-by: Sateesh_Peri <[email protected]> * Update modules/nf-core/seqcluster/collapse/tests/main.nf.test Co-authored-by: Sateesh_Peri <[email protected]> * Update modules/nf-core/seqcluster/collapse/meta.yml Co-authored-by: Sateesh_Peri <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]> * Add PREFIX to SPADES warnings log (#6615) * Update main.nf * Update main.nf.test.snap * Update actions/setup-java digest to 2dfa201 (#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 (#6618) * Fix bash failing if nothing to move in output directory (which is a valid behaviour) * HarshilAlignmentTM * Fix fq/generate (#6610) Update snapshot, add stub * Fix `seqcluster` (#6616) * change test data with smrnaseq data and fix fastq capturing * point to nf-core repo * add pairhmm threads to haplotypecaller (#6620) * Nextclade vers bump (#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]> * Add optional config mode in `mirtrace/qc` (#6623) * add optional config file * update mirtrace/qc * new module gatk/variants2table (#6619) * gatk/variants2table * Update modules/nf-core/gatk4/variantstotable/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * fix for https://github.com/nf-core/modules/pull/6619 * add optional file arguments This is a suggestion to add additional optional file arguments per the modules guidelines: https://nf-co.re/docs/guidelines/components/modules#required-and-optional-input-files These suggestions are untested. I did not add the [gatk_config_file](https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable#--gatk-config-file) argument. My current opinion is that the type of settings this would control are best set elsewhere. * update add args, update tests * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <[email protected]> * fix md5 --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Chase Mateusiak <[email protected]> * Split deepvariant 3 (#6172) * Move DeepVariant into a subcommand module rundeepvariant, preparing for split modules The test snapshot is updated because the process name in the version file changed. * Add a split DeepVariant workflow with individual processes for each step * Remove hash unique ID and fix input structure issue * Fixes for call_variants outputing sharded file * Fix test * Remove --channels insert_size, which is only applicable for short read data The channels should be specified in the pipeline config * Replace the model type value input with ext.args config * Fix tests: should run twice for two samples in input channel * Fix linting issues and input channel description * Fix formatting of md files Co-authored-by: Felix Lenner <[email protected]> * Corrections / imrpovements from @fellen31 review * Check tfrecord file names * Updating conda skipping options, because the paths have changed * Add deprecation warning for top-level process and test for the deprecated process * also skip conda for the new deprecated module --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * 4451 add vcf2maf nf test (#4463) * add nf-test case for vcf2maf without VEP * add VEP test case for vcf2maf nf-test * update linting for vcf2maf * fix prettier for vcf2maf * remove pytest files for vcf2maf * remove vcf2maf from pytest modules yml * add modules/nf-core/vcf2maf/tests/tags.yml * add line count to vcf2maf test * add line number and versions contents yaml to vcf2maf test * remove alternate container from vcf2maf testing and use the same container for testing with or without VEP * update modules/nf-core/vcf2maf/tests/main.nf.test * update modules/nf-core/vcf2maf/tests/main.nf.test * Update and fix tests * Apply suggestions from code review Co-authored-by: Simon Pearce <[email protected]> * Add conda declaration to nf-test * Remove output in snapshot * Add versions to snapshot --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Adam Talbot <[email protected]> * Update mirtop modules and subworkflow (#6635) * add arity to mirtop/gff * add prefix to mirtop output * update tests and snapshots * update yml * Add bcftools/pluginimputeinfo (#6624) * Add bcftools/pluginimputeinfo * Remove TODO * Change label * Update meta.yml --------- Co-authored-by: James A. Fellows Yates <[email protected]> * Get HISAT2 version from CLI (#6634) fix: Get version from cli * Fix tximport summarizedexperiment (#6638) * SummarizedExperiment: don't sanitise column names * tximport: explicitly disable name sanitisation * MEGAHIT: Add support for multi-libraries, export log (#6632) * Add support for coassembly, export log * Fix formatting * teensy bit more * New module jvarkit/wgscoverageplotter (#6633) * wgscoverageplotter * Apply suggestions from code review Co-authored-by: Maxime U Garcia <[email protected]> * fix meta * change snap * fix tags * fix env.yml * Apply suggestions from code review Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Add openmsthirdparty/cometadapter (#6627) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * Update output to use type dir for compatibility with tes. (#6645) Update output to use type dir for commpatibility with tes. * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.5 (#6642) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * minor changes to fastq preprocessing (#6643) * minor changes to fastq preprocessing * Update main.nf * Update bcftools/pluginimputeinfo meta.yml (#6646) Update meta.yml * Fix GTDBTK version calling in stub test (#6649) Use the proper version calling now implemented * flye: fix nf-test, update module (#6613) * fix nf-test, update module * Update nextflow.config * Update nextflow.config * update test * small hifi dataset * remove raw tests --------- Co-authored-by: Simon Pearce <[email protected]> * Add module openms/idmassaccuracy (#6647) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * add idmassaccuracy module * shorten version parsing --------- Co-authored-by: Simon Pearce <[email protected]> * Stop nf-test complaining about missing dependency (#6652) * Finish filepaths * Fix tags * Added nf-test for untarfiles (#6412) * Added nf-test for untarfiles * Matched conda versions with docker/singularity using wave containers * Changed test name * Added deprecation message * Remove custom params in GTDBTK/CLASSIFYWF (#6651) * Use the proper version calling now implemented * Remove custom params * Fix test * Add UPP (#6546) * Add UPP * fix lint * Update UPP * fix prettier * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * fixes * update * update tests * update * update * Update modules/nf-core/upp/align/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Usman Rashid <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Lili Andersson-Li <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: YSims <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Chris Wyatt <[email protected]> Co-authored-by: Luisa Santus <[email protected]> Co-authored-by: Francisco Martínez <[email protected]> Co-authored-by: fmartinez <[email protected]> Co-authored-by: FernandoDuarteF <[email protected]> Co-authored-by: Pieter Moris <[email protected]> Co-authored-by: Matthias De Smet <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Ömer An <[email protected]> Co-authored-by: Franziska Bonath <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Lucía Peña-Pérez <[email protected]> Co-authored-by: Lucpen <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: MargotCh <[email protected]> Co-authored-by: Krešimir Beštak <[email protected]> Co-authored-by: Chiara Schiller <[email protected]> Co-authored-by: Miguel A. Ibarra-Arellano <[email protected]> Co-authored-by: Krešimir Beštak <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Eric Wei <[email protected]> Co-authored-by: Sateesh <[email protected]> Co-authored-by: Pierre Lindenbaum <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Daniel Lundin <[email protected]> Co-authored-by: Nur M Shahir <[email protected]> Co-authored-by: shahirnm <[email protected]> Co-authored-by: Chase Mateusiak <[email protected]> Co-authored-by: Marius Bjørnstad <[email protected]> Co-authored-by: Stephen Kelly <[email protected]> Co-authored-by: Adam Talbot <[email protected]> Co-authored-by: Jonas Scheid <[email protected]> Co-authored-by: Venkat Malladi <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> * update JSON schema for modules meta.yml (#5837) * update JSON schema for modules meta.yml * add identifier and ontologies to the modules meta.yml JSON schema * remove qualifier --------- Co-authored-by: Phil Ewels <[email protected]> * Bulk update meta yml modules (#6015) * Update Abricate to include (missing) additional optional input channel and add stub (#5849) * Add missing optional input channel to abricate * Update abricate module to include missing optional input path * Update modules/nf-core/abricate/run/tests/main.nf.test Co-authored-by: Carson J Miller <[email protected]> * Fix linting * Update modules/nf-core/abricate/run/main.nf * Get downstream module test --------- Co-authored-by: Carson J Miller <[email protected]> * Fix custom/catadditionalfasta (#5851) * Update environment.yml * Update main.nf * update to samtools 1.20 (#5852) * update to samtools 1.20 * keep samtools 1.19.2 for now * update snapshot * [automated] Fix linting with Prettier * keep 1.20 afterall * update snapshot --------- Co-authored-by: nf-core-bot <[email protected]> * Update input params for bwameme (#5853) * update recipe * update rthreads * update tests * Update meta.yml * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 (#5857) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * `--output-unselected` option in `samtools view` (#2674) * add unoutput option * trying to fix emit * CI fixed, tests still incorrect * Fixed the checksums * Fixed the syntax * Call this "unselected" rather than "unoutput" * Alignment rocks * bugfix: the variable needs to be visible by the output declaration * bugfix: this was not the regular file name * Updated the test case * fixup! Alignment rocks * Updated the meta.yml --------- Co-authored-by: Matthieu Muffato <[email protected]> * stubs and test for rnaseq modules - part I (#5854) * stubs and test for bbmap_bbsplit * add test for index * add stubs for custom/catadditionalfasta * add stubs for fq/subsample * add stubs for hisat2/extractsplicesites * update fastq_align_hisat2 snapshot * add stubs for hisat2/build * add stubs for hisat2/align * more stubs bbmap/bbsplit * add stubs for preseq/lcextrap * more stubs for fq/subsample * proper stubs for hisat2/align * remove old snaps * Remove CUTUPFASTA from pytests * Revert "Remove CUTUPFASTA from pytests" This reverts commit 0fa8c1bd400ddc4c80c94cbb59f131d8a43f57b3. * Bump concoct/cutupfasta version, add stub, add nf-test (#5864) * Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting * Adding meta to multivcfanalyzer, updating test to nf-test (#5773) * Adding meta to multivcfanalyzer, updating test to nf-test * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <[email protected]> * fix meta.yml * Add sort to vcfs * Add tab to tags * add checks for files due to failing md5 sums across docker,conda,singularity --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Concoct/concoctcoveragetable modules updates (#5868) * Bump concoct/cutupfasta version, add stub, add nf-test * Bump conda build, add stub and nf-test for CONCOT/concoctcoveragetable * Remove pytest entry --------- Co-authored-by: Aida Andrades Valtueña <[email protected]> * Added stub logic and test to fastq_fastqc_umitools_fastp (#5858) * Added stub logic and test to fastq_fastqc_umitools_fastp * Now emitting trimmed reads * Adding input value-channel for controlling spring-decompress cmd and output (#5850) * Enable single fastq.gz-output from spring/decompress by setting meta.single_end or meta.one_strand * Controlling output with value-channel write_one_fastq_gz * Update modules/nf-core/spring/decompress/meta.yml Co-authored-by: Maxime U Garcia <[email protected]> * nf-test for spring/decompress * Trying to please linter * Trying to please linter --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * Update stranger (#5717) * everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <[email protected]> * mapAD: fix `versions.yml` emission (#5874) mapAD: fix `version.yml` emission * add stub and stub test to chromap, change test names (#5872) * add stub and stub test to chromap, change test names * add stub and stub test to chromap, change test names * change setup * move setup out of test * move * produce stub files (#5875) * chore(deps): update pre-commit hook python-jsonschema/check-jsonschema to v0.28.6 (#5878) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * update peddy tests (#5880) update peddy * Update main.nf (#5870) * Update main.nf VEP html report is missing when publishing results because by default vep html file is `_summary.html` instead of `.summary.html`. This changes just adjust the module to the vep defaults to avoid the issue. * Updated html pattern in VEP to be more generic * bump MultiQC version (#5884) bump MQC * Bump shinyngs modules (#5881) * Bump shinyngs modules * Bump versions for snapshot * Update CONCOCT module(s): conda build bump, stub, and nf-test (#5869) * Version update, stub, nf-test for concoct/concoct * Bump version, add nf-test, stub to concoct/mergecutupclustering * nf-test, stub, and version conda build version bump for concoct/extrafastabins * Remove a superfluous config and specify a used one * Update modules/nf-core/concoct/extractfastabins/main.nf Co-authored-by: Simon Pearce <[email protected]> * Remove superfluous config file * Clean up code * Repair all stub tests that were empty --------- Co-authored-by: Simon Pearce <[email protected]> * `fasta_binning_concoct` subworkflow: do not fail on join (#5824) * fix: do not fail on mismatch for samples not binned with concoct * Migrate to pytest * Improved Harshil alignment --------- Co-authored-by: James A. Fellows Yates <[email protected]> * new module: datavzrd (#5883) * Generated structure for new module * Implemented module * Added semi-functional tests * Cleaned tests - test don't work yet * fix main, start nf-test * add new test data * fix linting * try to assert folders * fix tests * change output to prefix * change to prefix * update to prefix --------- Co-authored-by: vickylaram <[email protected]> * samtools/reheader: Fix bug causing output name to be incorrectly evaluated (#5887) Fix bug causing output name to be incorrectly evaluated * nf-test for snpsites (#5284) * nf-test for snpsites * remove old pytest * Delete modules/nf-core/snpsites/tests/nextflow.config * Update modules/nf-core/snpsites/tests/main.nf.test Co-authored-by: Joon Klaps <[email protected]> * Update assert Co-authored-by: Joon Klaps <[email protected]> * renamed test Co-authored-by: Joon Klaps <[email protected]> * reverted the input * updated input...again Co-authored-by: Joon Klaps <[email protected]> * fixed typo Co-authored-by: Joon Klaps <[email protected]> * Regenerate snapshot and fix linting --------- Co-authored-by: Joon Klaps <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Added prefix to gunzip and while keeping the default name as `archive.toString() - '.gz'` (#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda * add dedicated output channel for trimmomatic stderr log (needed for multiqc) (#5501) * created new output channel capturing stderr of trimmomatic * updated output channel for trimmomatic * Add stub test and update snapshots * Add stub and update tests * Fix linting and add tee --------- Co-authored-by: John Palmer <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> * `ariba/getref` port to nf-test, add meta to tuple and stub (#5877) * port to nf-test, add meta to tuple and stub * modify meta and fix tags * change from each to tuple * Pass annotation files to last-dotplot (#5885) * Pass annotation files to last-dotplot The annotation of the target (plotted horizontally) genome is passed as a new channel. The annotation of the query (plotted vertically) genome is passed as a new component of the first channel. This is because this module typically loops on a list of alignments of various query genomes (from samplesheet) to a single target genome. The annotation files are called `annot_a` and `annot_b` because they are passed to the `-a` and `-b` arguments of `last-dotplot`. * Put arguments on separate lines. * Add meta map and reorder channels. * Test with dummy annotation files. Thanks @SPPearce for the hint. * Add meta to bowtie build (#3848) * Add meta to bowtie build * Swap fastq ngscheckmate tests * Swap to nf-test * Remove spurious changes to bowtie2 * Actually revert bowtie2 * Add the rest of bowtie2 * Again * Revert bowtie2 changes * Swap to meta.id as prefix * Swap bowtie align to nftest * Update tests * Use nft-bam * Update modules/nf-core/bowtie/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Swap to testdata path * Update modules/nf-core/ngscheckmate/patterngenerator/main.nf * Swap index finding to $ * Fix vafncm test * Update meta * Remove bam header md5sum * Update fastq test * Update paired bam test * Delete modules/nf-core/bowtie/align/tests/nextflow.config --------- Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * nf-test for pilon (#5293) * nf-test for pilon * linting for license * Add stub and extra test * Swap to testdata_base_path * Add missing END_VERSIONS and alignment * Add optional outputs to stub --------- Co-authored-by: Simon Pearce <[email protected]> * Bump phantompeakqualtools 1.2.2 (#5889) * Add stub section * Update yml * Add nf-test * Get rid of pytest * Make lint happy * Update tests * Update tests to make lint happy * update tests * Make lint happy * Using the same version as CI of nf-test locally might be a good idea * Use wave images * Make lint happy * Simplify tests --------- Co-authored-by: Simon Pearce <[email protected]> * Added variance filtering to custom/matrixfilter (#5358) * Added variant filtering to matrix filter * Corrected indentation * Simplified function in single conditional block * fixed line indentation * Fixed whitespace * Fixed logic * line wrapping change * added whitespace around comments * [automated] Fix linting with Prettier * remove trailing whitespace * Update matrixfilter.R * Remove whitespace --------- Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Simon Pearce <[email protected]> * Update md5sum module to be able to take multiple files (#3610) * Fix version string spurious text in singularity tests * Add config for subworkflow * Update md5sum module to work with multiple files * linting * Fix stub * Add option to generate single file * Update modules/nf-core/md5sum/main.nf Co-authored-by: Matthieu Muffato <[email protected]> * Simplify versions processing --------- Co-authored-by: Matthieu Muffato <[email protected]> * Add share to find path (#5899) * build: Bump deepvariant to 1.6.1 (#5801) * build: Bump deepvariant to 1.6.1 * interim dir not allowed to be a dot in 1.6 * Update modules/nf-core/deepvariant/main.nf Co-authored-by: Maxime U Garcia <[email protected]> * hack: Hard code version https://github.com/google/deepvariant/issues/830 --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> * bump somalier/extract and somalier/relate version (#5894) * bump version * nf-test migratino * revert ancestry * fix linting * Update snap * fix unicode space --------- Co-authored-by: Simon Pearce <[email protected]> * Added evigene/tr2aacds (#5898) * Added evigene/tr2aacds * Sorted file list and added activation script * Fixed issues raised by feedback * correct president stub (#5904) * correct president stub * Large update to module * Update prefix and meta --------- Co-authored-by: Simon Pearce <[email protected]> * Fix EClint errors (#5907) Fix EClint * New module: nanoq (#5896) * Add the new module nanoq * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <[email protected]> * define the output_format * Update modules/n…

SPPearce and others added 13 commits November 14, 2022 09:27

Fix version string spurious text in singularity tests

e70d080

Merge branch 'nf-core:master' into master

8e7a7a8

Merge branch 'nf-core:master' into master

c63c3ca

update to main nf-core

aec8f2c

Merge branch 'nf-core:master' into master

ea42b9d

Merge branch 'nf-core:master' into master

2ad2dbf

Merge branch 'nf-core:master' into ngscheckmate_workflow

1ca507d

Add config for subworkflow

ad13c7a

Merge branch 'ngscheckmate_workflow' of https://github.com/SPPearce/m…

b090eb7

…odules into ngscheckmate_workflow

Merge branch 'nf-core:master' into ngscheckmate_workflow

97be67e

Merge branch 'nf-core:master' into ngscheckmate_workflow

a613cec

Merge branch 'nf-core:master' into ngscheckmate_workflow

49b90cd

Update md5sum module to work with multiple files

adf50fd

SPPearce changed the title ~~Md5sum~~ Update md5sum module to be able to take multiple files Jul 7, 2023

SPPearce and others added 3 commits July 7, 2023 14:34

Merge branch 'master' into md5sum

467b2ad

linting

6ff4b9c

Merge branch 'md5sum' of https://github.com/SPPearce/modules into md5sum

8866e27

SPPearce marked this pull request as draft August 29, 2023 13:17

SPPearce added 2 commits June 22, 2024 21:23

Resolve merge

15b2c5a

Fix stub

309793a

SPPearce added the Ready for Review label Jun 22, 2024

SPPearce marked this pull request as ready for review June 22, 2024 22:09

SPPearce requested a review from matthdsm as a code owner June 22, 2024 22:09

SPPearce requested a review from mahesh-panchal June 26, 2024 21:37

mashehu approved these changes Jun 27, 2024

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muffato reviewed Jun 27, 2024

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Merge branch 'master' into md5sum

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mahesh-panchal reviewed Jul 1, 2024

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Add option to generate single file

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Merge branch 'master' into md5sum

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mahesh-panchal reviewed Jul 1, 2024

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mahesh-panchal approved these changes Jul 1, 2024

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muffato reviewed Jul 1, 2024

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Update modules/nf-core/md5sum/main.nf

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Co-authored-by: Matthieu Muffato <[email protected]>

SPPearce enabled auto-merge July 1, 2024 12:28

Simplify versions processing

25ef266

SPPearce added this pull request to the merge queue Jul 1, 2024

Merged via the queue into nf-core:master with commit 1164836 Jul 1, 2024
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SPPearce deleted the md5sum branch July 1, 2024 12:46

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Update md5sum module to be able to take multiple files #3610

Update md5sum module to be able to take multiple files #3610

SPPearce commented Jul 7, 2023 •

edited

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SPPearce commented Jul 1, 2024

Update md5sum module to be able to take multiple files #3610

Update md5sum module to be able to take multiple files #3610

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SPPearce commented Jul 7, 2023 •

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