Use the viash dependencies config value for workflows #606
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…endencies-config-value-for-workflows
…endencies-config-value-for-workflows
…endencies-config-value-for-workflows
…endencies-config-value-for-workflows
…endencies-config-value-for-workflows
rcannood
requested changes
Jan 8, 2024
…endencies-config-value-for-workflows
…he-viash-dependencies-config-value-for-workflows
…s into 604-use-the-viash-dependencies-config-value-for-workflows
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
rcannood
approved these changes
Jan 12, 2024
…endencies-config-value-for-workflows
…endencies-config-value-for-workflows
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@ddemaeyer Did you want to test these workflows before merging the PR? |
…endencies-config-value-for-workflows
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As discussed with @ddemaeyer, lets merge this 👍 |
…endencies-config-value-for-workflows
DriesSchaumont
deleted the
604-use-the-viash-dependencies-config-value-for-workflows
branch
VladimirShitov
pushed a commit
that referenced
this pull request
Mar 12, 2024
* Update schema for Viash 0.8.0 * Update bbknn_leiden * Fix using depdencies in bbknn_leiden workflow * Update harmony_leiden workflow to use dependencies * Update initialize_integration workflow * Update scanorama_leiden workflow * Update scvi_leiden workflow to use dependencies * Rework totalvi_leiden workflow to use dependencies * Rework rna_multisample pipeline to use dependencies * Update qc workflow to use dependencies * Update demux workflow to use dependencies * Update conversion workflow to use dependencies * Update cellranger_postprocessing workflow to use dependencies. * Update cellranger_multi workflow to use dependencies * Update cellranger_mapping workflow to use dependencies * Update bd_rhapsody workflow to use dependencies * Update make_reference workflow to use State functionality and use dependencies * Implement dependencies for final workflows * Update CHANGELOG * Move split stub into main.nf file so that it can be found when running from target * Enable workflow builds in CI * Do not add docker info for workflows in CI * Undo changes to CI * Try fix branch * Also add to other setup * Revert dec943d..a39e317 * Use develop_0_8 version of viash * Override container registry for publishStatesProc in config. * Revert "Override container registry for publishStatesProc in config." This reverts commit ccc0b91. * Update src/workflows/multiomics/rna_multisample/integration_test.sh Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Move from ConcurrentHashMap to Immutable hashmap * Update src/workflows/multiomics/multisample/main.nf Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Fix second multisample workflow test * Uniformize rna_multisample and prot_multisample, remove erroneous output check. * Fix qc workflow namespace * Fix running full pipeline with -stub * Update src/workflows/multiomics/multisample/main.nf Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * `calculate_qc_metrics`: add multiple arguments to config Adding the arguments allows not only for the user to specify the output names of the columns, but also disable the generation of statistics if desired. * Add PR number to CHANGELOG * Use qc pipeline everywhere when calculating qc statistics * Undo change to viash project config * Update CHANGELOG * Remove changes to main-build CI related to viash version * Bump viash to 0.8.3 * Add test for changing output column * Change argument names * Merge origin/604-use-the-viash-dependencies-config-value-for-workflows into 604-use-the-viash-dependencies-config-value-for-workflows * Leftovers for fbecfc4 * conversion pipeline: avoid storing component in state * demux pipeline: use runEach * make_reference workflow: use component.config.functionality.name * full_pipeline: use component.config.functionality.name * Update src/workflows/multiomics/integration/totalvi_leiden/main.nf Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/workflows/multiomics/multisample/main.nf Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/workflows/multiomics/rna_singlesample/main.nf Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Fix integration tests --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
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Changelog
Use the viash dependencies config value for workflows
MERGE #644 FIRST!Issue ticket number and link
Closes #603
Closes #604
Closes #596
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!