Updated test data paths batch 11 #6085
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GallVp
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rpetit3,
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SPPearce
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Aug 2, 2024
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The freyja conda module might need an extra dependency pinning to fix the subworkflow failure. |
Joon-Klaps
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Aug 2, 2024
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Updated test data paths
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This is failing repeatedly. I'll investigate on my machine and then update it. |
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The issue with |
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* Updated test data paths * Added --depthcutoff for freyja/boot
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* Module: ichorcna/run updated to v0.5.0 Changes: - ichorcna no longer has a CLI, so it has been updated to use native R - Some additional parameters have been added - Requires scStates option in nextflow.config or it crashes * ichorcna/run gc_wig not optional * ichorcna/run centromere put above other parameters as it is more important * ichorcna correct test URLS * fix meta.yml and change the name to normal_background * [automated] Fix linting with Prettier * Update environment to 0.5.0 * createpon test * Swap to nftest and test 0.5.1 docker * Remove from tests * Reset test.yml * Update output channels and snapshot * Update snap and meta * Update PoN * Add stub and additional asserts to PoN * change output directory of bclconvert & bcl2fastq (#6112) * change output directory * fix linting * update snapshot * update lane * delete environment.yml * Updated test data paths batch 11 (#6085) * Updated test data paths * Added --depthcutoff for freyja/boot * Updated test data paths batch 17 (#6103) Updated paths * Updated test data paths batch 19 (#6105) * Updated paths * Updated shapshot for liftlong * chore(deps): update actions/setup-java digest to 6a0805f (#6114) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Updated test data paths batch 18 (#6104) * Updated test data paths batch 18 * Fixed instrain version in conda file * Fixed instrain version in conda file * Removed db content md5 from snapshot to pass conda test * Added samtools to instrain env * Updated snapshot * Bump chromap version to chromap modules (#6113) * Bump chromap version to chromap/index * Bump chromap version to chromap/chromap * Use nft-bam as suggested in review * Change how prefix for output index is set to be modifiable * Add stub, nf-tests and bump version 3.5.5 to deeptools modules (#6109) * Update deeptools/plotheatmap * Update deeptols/multibamsummary * Update plotpca * Update deeptools/computematrix * Update deeptools/bamcoverage * Remove comment * Update deeptools/plotcorrelation * Fix c/p error * Update deeptools/plotfingerprint * Update nf-core/deeptools * Add deeptools/plotprofile snapshot * Simplify tests and fix some issues * Make lint happy * Make lint happy * Reverting plotheatmap meta.yml * Fix input declaration in meta yaml * Fix multibamsummary tags * Fix value type in meta.yml * Remove pytest for deeptools modules * Add missing tags in compound test runs * Fix tyop * Apply review suggestions * Update modules/nf-core/deeptools/bamcoverage/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update snapshot for deeptools/bamcoverage after applying review suggestion * Change how prefix for output index is set to be modifiable * Revert last commit (wrong branch) :P --------- Co-authored-by: Simon Pearce <[email protected]> * Bracken bug fix (#6119) * Allow for construction of standard database * Update meta to include standard database * Fix bug for passing in -l with ext.args * Full correction * Update test snapshots * Add test corresponding to the genus issue * Revert "Allow for construction of standard database" This reverts commit 71b800e. * Revert "Update meta to include standard database" This reverts commit 1d48333. * Add nf-test to krakentools/combinekreports (#6120) add nf-test to krakentools/combinekreports --------- Co-authored-by: Adam Talbot <[email protected]> Co-authored-by: Adam Talbot <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Anabella Trigila <[email protected]> Co-authored-by: Usman Rashid <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco <[email protected]> Co-authored-by: Ezra Greenberg <[email protected]> Co-authored-by: Lili Andersson-Li <[email protected]>
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda