Update and nf-test sentieon/tnscope and sentieon/tnhaplotyper2 #8283
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Removed call to toFloat, to keep memory value integral
* accommodate more outputs * Update main.nf * Update meta.yml * update nf-test assertions and snapshot * fix bam test --------- Co-authored-by: Anne Marie Noronha <[email protected]> Co-authored-by: Juan Blanco Heredia <[email protected]>
* updated freyja update to latest version * updated freyja variants to latest version * updated freyja boot to latest release * updated freyja demix to latest release * fix freyja update and variants with fixed bioconda recipe * updated snapshot for subworkflow after freyja update * fixed meta.yml for freyja update * correctly updated freyja boot container and snapshot
* updated bcftools annotate to latest version * updated bcftools call to latest version * updated bcftools concat to latest version * updated bcftools consensus to latest version * updated bcftools convert to latest version * updated bcftools csq to latest version * updated bcftools filter to latest version * updated bcftools index to latest version * updated bcftools isec to latest version * updated bcftools merge to latest version * updated bcftools mpileup to latest version * updated bcftools norm to latest version * updated bcftools pluginimputeinfo to latest version * updated bcftools pluginscatter to latest version * updated bcftools pluginsplit to latest version * updated bcftools plugintag2tag to latest version * updated bcftools query latest version * updated reheader query latest version * updated roh query latest version * updated sort query latest version * updated split query latest version * updated stats query latest version * updated bcftools view latest version * updated snapshot for bam_ngscheck mate after bcftools update * added required tags to pass linting * fixed bam_ngscheckmate to pass linting * Fix bam_ngscheckmate --------- Co-authored-by: Simon Pearce <[email protected]>
…re#7233) * Add functionality for `--unknown-slide` option Add functionality to be able to use the `--unknown-slide` option of Space Ranger Count, specified using the `slide` column in the input samplesheet. * Fix tests snapshots for spaceranger/count * Update Docker image location and version * Update README with Docker image location / version * Add stubs for spaceranger/[mkref/mkgtf] * Minor formatting * Add stub code for spaceranger/mkgtf * Update spacreranger snapshots * Remove obsolete snapshots in spaceranger/counts * Fix snapshots * Update spaceranger/mkref snapshots * Add slide/area as inputs instead of meta values Add the slide and area values as module inputs instead of meta values (i.e. `meta.slide` and `meta.area`) as before, as this does not follow the module guidelines. Also update `meta.yml` and tests accordingly. * Fix erroneous test inputs * Ignore Dockerfile as module name * use uv & update filter pattern * fix syntax error * Revert "use uv & update filter pattern" This reverts commit f4daa56. * update subworkflow filter * Update .github/workflows/lint.yml Co-authored-by: Júlia Mir Pedrol <[email protected]> --------- Co-authored-by: Sateesh_Peri <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Christophe Avenel <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]>
Add threads for all seqkit modules missing (and language server autoformatting)
…ules (nf-core#8171) * refact: update structure of `variancepartition/dream` * refact: allow formula in channel inputs * docs: add formula to meta * fix: unstable digits in limma modules * Apply suggestions from code review Co-authored-by: Jonathan Manning <[email protected]> * refact: use formula in `variancepartition/dream` only * docs: remove meta example --------- Co-authored-by: Jonathan Manning <[email protected]>
* add module integronfinder * I fix the issue of unstable snapshot * I fix the issue of identifier in meta.yml file * Update modules/nf-core/integronfinder/main.nf Co-authored-by: Louis Le Nézet <[email protected]> * I specify only the information about the version rather than the others and update the content of yml file * I remove the optional command arguments * update test to avoid unprintable char * I update the optional extention and fix mismatched hashes * I fixed the unbound variable error of CONDA_PREFIX * I fixed the unbound variable error of CONDA_PREFIX of stub * I update ontologies and remove snapshot content of files * I update the version.yml snapshot * I change the command for version extraction and modify the assert * I update the stub, the assert and fix the lint error * I update the assert snapshot for two outputs * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]> * Update modules/nf-core/integronfinder/tests/main.nf.test Co-authored-by: Louis Le Nézet <[email protected]> --------- Co-authored-by: Louis Le Nézet <[email protected]>
* add gpu snapshot updater action * remove sention
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* updated mindagap stubs and tests * fix numpy version
…ore#8196) * fixed bug in bandage/image module, wrong versions.yml outputted * update fix just for versions generation
Co-authored-by: Sofia Stamouli <[email protected]>
* add nf-test and stub * gather caller info using meta * lint * update version * change conda version * remove tag from conda * update conda image * fix bad indentation * renew bioconda image * skip conda * skip conda in nf-test
* update vep to 113.4 and redo conda tests * also unskip vep subwf
* fix typo * fix one more typo in snapshot updater
* change MUSE_SUMP to high memory module * update version string * fix meta * change to avoid empty vcf * change version accession * upgrade muse call to process_high * upgrade muse sump to process_high
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Update input tuple; cleanup stub * Update meta.yml for poolsnp
* Update modkit and porechop modules * update link to porechop singularity container * update link --------- Co-authored-by: ra25wog <[email protected]>
* Add metaspace/download module and fix issues from Bishoy's feedback(nf-core#8145) * added stub * change environment.yml bioconda::metaspace2020 --------- Co-authored-by: Bishoy Wadie <[email protected]>
* Swap vrhyme/extractunbinned to nf-test * Swap linkbins to nf-test, add ontology, automatically gunzip * Fix linting * Update snapshot * Update modules/nf-core/vrhyme/vrhyme/meta.yml
* Begin migration for cellrangerarc/count * Tidy up whitespace * cellrangerarc/count full test working * Commiting broken stub test on purpose * Remove redundant config * Turn off Conda tests in CI * Add nextflow.config * Add single whitespace to add this file to CI tests * Revert "Add single whitespace to add this file to CI tests" This reverts commit 39b7f4c. * Revert "Revert "Add single whitespace to add this file to CI tests"" This reverts commit f65f635. --------- Co-authored-by: Sateesh_Peri <[email protected]>
* better assertion and stub tests * polish * capture versions better * fix paths
* module without test * LINKS test * assert names of files that are not snapshotted * review comments * no zcat magic :( * more tests, switched to gzip instead of zcat
* Migrate to nf-test * Sort output --------- Co-authored-by: LouisLeNezet <[email protected]>
remove plink2 hwe
* Migrate to nf-test * Update prefix --------- Co-authored-by: LouisLeNezet <[email protected]>
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SPPearce
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Apr 11, 2025
This was
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Apr 12, 2025
SPPearce
requested review from
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Swapping both
sentieon/tnscopeandsentieon/tnhaplotyper2to nf-test.While I was there, I updated tnscope to be more consistent with the ordering used in tnhaplotyper2 (splitting out the indices for instance).