Update ichorcna to v0.5.1 and nf-test #6079
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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
14 tasks
* change output directory * fix linting * update snapshot * update lane * delete environment.yml
* Updated test data paths * Added --depthcutoff for freyja/boot
Updated paths
* Updated paths * Updated shapshot for liftlong
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* 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/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
* 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]>
* 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
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