Sourcepredict changes #7103
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Sourcepredict changes #7103
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edited nextflow.config
Edited the test file
* update module * remove pytest --------- Co-authored-by: Carson J Miller <[email protected]>
* remove for loop * Update subworkflows/nf-core/utils_nfcore_pipeline/main.nf Co-authored-by: Matthias Hörtenhuber <[email protected]> --------- Co-authored-by: Matthias Hörtenhuber <[email protected]>
#6767) * Change centrifuge build to export a directory of all the files (like other reference building/database building modules) * Fix meta.yaml linting
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* use multi-line string for warning * fix star/align meta.yml information
* update container version-tag * update snapshots * bump conda versions
…6773) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* start filling in mneta * Fix linting * Replace switch with ifelse * Fix ype in in if else
* allow multiple abund files * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/maxbin2/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> --------- Co-authored-by: James A. Fellows Yates <[email protected]>
* Fix usage of empty versions channel from trimming * Fix snap
* update bismark v0.24.2, rm input stageAs, add stub, update tests+snap * udpate bismark/genomepreparation tests * update bismark/align main to take separate fasta and update tests+snap * update bismark/methylationextractor main, tests+snap * update bismark/coverage2cytosine main, tests+snap * update bismark/deduplicate main, tests+snap * typo fix * bismark/report/ update main, stub tests+snap * bismark/summary update ver, +stub, tests+snap
* New module: deepvariant/vcfstatsreport * Add stub tests * exclude conda tests * Update main.nf Single thread.
* update malt/build module * use stageAs for input fasta files * Try HTTPS rather than s3 * Trying manually restricting memory * Move config loading to the right place * Update modules/nf-core/malt/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update main.nf.test * Update nextflow.config * Get tests running * Adjust to VM minimum * And MALT_RUN * use process.resourceLimits defining the memory limit * Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update nextflow.config --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
* move mafft to mafft_align * add mafft guidetree * update mafft align * add mafft guidetree tests * fixes * up * update other mafft tests * update mafft * fix * don't lint deleted files * filter out main.nf.test and main.nf.snapshot * try different strategy * fix other * fix other * add tests * remove pytest * up * update nftest * fix --------- Co-authored-by: mashehu <[email protected]>
* remove pigz * add fix line * test
prettier
* update trinity version and snapshot * use commas in file extension pattern --------- Co-authored-by: Sateesh_Peri <[email protected]>
* Add module gzrt (#6918) * fixed environment.yml * Reply to review * gzrecover and gzip oneliner * gzrt uses a named pipe to avoid temp files --------- Co-authored-by: tm4zza <[email protected]>
* adding mgikit * fix style * fix docker link * fix style * fix meta info * fix meta info * fix meta info * fix meta info * adding tests * fix typo * update meta * update meta * lint module * Update modules/nf-core/mgikit/demultiplex/main.nf Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * fix tests * Update modules/nf-core/mgikit/demultiplex/main.nf --------- Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
* Add sylph sketch * Update snap * Update snap * Remove sylph profile * Fix linting with version * Fix output format in meta.yama * Fix input formatting * Update meta * Fix input formatting * Fix output formatting * Add versions to output * Update snap * Update test * Fix lintinG * Test linting * Linting * Correct output names * Add quotes to output names * Linting * Fix align in input * Update modules/nf-core/sylph/sketch/tests/main.nf.test Co-authored-by: Sateesh_Peri <[email protected]> * Update snapshot * Add stub test --------- Co-authored-by: Sateesh_Peri <[email protected]>
* bump hifiasm version * snap
* Attempt at fixing samshee module with latest release * Fixed container urls * Fixed snaps with version
* Update gawk for compressed output * Update nf-test and linting --------- Co-authored-by: LouisLeNezet <[email protected]>
* spaceranger_bump_version * build: Use ADD to download tar.gz * style: Clean up Dockerfile * chore: Update labels and use an ARG * chore: Switch base image to match Seqera Containers * build: Make a manual checksum * chore: Update [email protected] * docs: Update documentation * build: Bump image location and tag * build: Can't actually get run of the tar.gz unzip step Because of the Spaceranger URL. * test(spaceranger): Add stub for mkref * test: Bump snapshot * test: Update versions yaml snapshot * docs: Use a placeholder to avoid confusion Co-authored-by: sebotic <[email protected]> --------- Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: sebotic <[email protected]>
* update propd module * it works, need to add test * create empty file when no DE genes were found; nf-test for permutation setting works * modified propd module to save pairwise results optionally, and save empty output when no DE genes were found * added additional tests in propd module * round digits for reproducibility matters * updated the test snapshots for propd * update meta * add description to meta * fix meta * lint propr/propd * updated container for propr/propd * update test snapshots for propr/propd * [propr/propd] update container and snapshots * [propr/propd] fix bug when defining the test configs * [propr/propd] fix bug: only round numeric columns * [propr/propd] update test snapshots * [propr/propd] update containers * [propr/propd] update test snapshots * [propr/propd] update singularity url
* Create module * parse arguments on module R script * update meta info * update nf-test * update snaps after upgrading versions file * update snaps after upgrading versions file * add stub test, meta components and update names * remove comments from ymls * change output * add meta to output channels * fix environment.yml linting * update snaps * replace Stub with stub to pass linting * Update main.nf.test * change normalise by normalize * move moduleBinaries to test nextflow config * update snapshot after renaming --------- Co-authored-by: Anabella Trigila <[email protected]>
* initialize module * update test * Remove TO-DO from main.nf.test * Remove comment from main.nf.test * update test after meta component in output channels * split channel into png and txt outputs * update meta file * move moduleBinaries to test nextflow config
…e tests (#7075) * Update the umi-tools dedup tests to use the new test data with UMIs. * Update umicollapse tests to use the new UMI test data. * Switch to nf-bam plugin for output validation. --------- Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Jonathan Manning <[email protected]>
remove unused code from utils_nfcore_pipeline swf
* init bwameth subworkflow * update output channels * bwameth single, paired-end default, skip_dedup tests * add GPU tests * separate GPU tests * add subworkflow GPU test path to test.yml include * add subworkflow GPU test path to test.yml include * add subworkflow GPU test path to test.yml include * use more descriptive collect variables than it * rename file to be explicit * separate profile exclusions * add gpu tag * rm old test.yml * add gpu test path to gpu-tests.yml:ci * Added log_level: DEBUG * Setup CI for debug * add more debug steps * usman's fix for exclude tags * Updated fail condition * ci sync to master * fix filtering by usman * Removed --changed-since when tags are supplied * Enabled more checks and added a non-gpu module * Two fixes * Now using paths * Fixed paths * Fixed typo * Now pass all paths instead of matrix * Added confirm pass, cleaned dispatch and removed DEBUG * Renamed all passes to confirm-pass * Now using adamrtalbot/detect-nf-test-changes * small ch format fix --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Usman Rashid <[email protected]>
Improve input condition Co-authored-by: Sateesh_Peri <[email protected]>
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PR checklist
nf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda