Bulk update meta yml modules #6015
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…l and add stub (nf-core#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]>
* Update environment.yml * Update main.nf
* 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 recipe * update rthreads * update tests * Update meta.yml
….10 (nf-core#5857) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* 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 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
This reverts commit 0fa8c1b.
* Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting
* 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]>
* 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 * Now emitting trimmed reads
…output (nf-core#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]>
* everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <[email protected]>
mapAD: fix `version.yml` emission
* 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
…a to v0.28.6 (nf-core#5878) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
update peddy
* 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 shinyngs modules * Bump versions for snapshot
…e#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]>
* 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]>
* 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]>
…uated (nf-core#5887) Fix bug causing output name to be incorrectly evaluated
* 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]>
….toString() - '.gz'` (nf-core#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda
…ultiqc) (nf-core#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]>
mirpedrol
requested review from
christopher-hakkaart,
scorreard,
peterpru,
BioInf2305,
LouisLeNezet,
nh13,
TCLamnidis,
heuermh,
sidorov-si,
hseabolt,
mjcipriano,
sateeshperi,
asp8200,
DonFreed,
luiskuhn,
SPPearce,
suzannejin,
phue,
muffato,
louperelo,
nevinwu,
lescai,
JackCurragh,
maxibor,
thanhleviet and
mahesh-panchal
as code owners
luisas
approved these changes
Sep 19, 2024
mirpedrol
added a commit
that referenced
this pull request
Sep 20, 2024
* 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…
herpov
pushed a commit
to herpov/modules
that referenced
this pull request
Oct 2, 2024
* 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…
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Close #4983
Close #5830
Updates the
meta.ymlof modules to the correct structure by using nf-core/tools after implementing nf-core/tools#3028 and nf-core/tools#3032The changes were generated by running
nf-core modules lint --all --fixNeeds updating the JSON schema which validates
meta.ymlfiles: #5837Same changes should be implemented for subworkflows.
Note
Open as a draft PR to avoid requresting review to code owners.