staging --> master #1496
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staging --> master #1496
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Updated documentation for Pairedtag, BuildIndices, and Optimus
* add peak calling * added output for peaks * fix * fix * test * remove ls * test * test * test * test * test * test * test * made another task * test * test * test * test * test * test * test * change a line * test * test * test * test * test * test * test * Add peakcall to task * test * add parameters * test * peak calling * remove bam_base_name from CreateFragments task * separate task for macs3 consistent with create fragments * Update atac.wdl update snap_atac_docker tag to 2.0.0 * snapatac2 updates * turn off createfragments peakcalling * remove peakcalling from createfragments and parameterize probability_threshold * remove probability_threshold parameterization * remove repeated line * Updated pipeline_versions.txt with all pipeline version information * add optional parameter * add output * add output * test * test * test * test * test * Added matrix as output * Updated pipeline_versions.txt with all pipeline version information * Added matrix as output * Added matrix as output * test * test * remove comments * update changelogs/versions * Updated pipeline_versions.txt with all pipeline version information * documenation * rename * rename * rename * rename * fix * fix * fix * fix * fix * fix * add peak call json * fix * fix * Updated pipeline_versions.txt with all pipeline version information * fix * fix * fix * fix * Updated pipeline_versions.txt with all pipeline version information * fix * fix * updating TestMultiome to run peak calling * update expected_cells and parameterize probability thresholds * expected cells as integer * fix * update probability_threshold * remove quotes around probability_threshold * remove typo * fix * fix --------- Co-authored-by: aawdeh <[email protected]> Co-authored-by: GitHub Action <[email protected]> Co-authored-by: ekiernan <[email protected]>
dev --> staging
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DO NOT SQUASH MERGE!!! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
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ExomeGermlineSingleSample: All errors in the VerifyMetrics ConsolidateErrors task ExomeReprocessing: Errors in the VerifyMetrics ConsolidateErros task WholeGenomeGerminlineSingleSample: All errors in the VerifyMetrics ConsolidateErrors task WholeGenomeReprocessing: Error in VerifyMetrics ConsolidateErrors Multiome: Errors in CompareATACBAMs and CompareATACLibrary metrics - all appear to be due to non-determinism Optimus: 8k_unstranded: Error in CompareH5ad, appears to be due to EmptyDrops, which is non-deterministic PairedTag: dev_10k_pbmc: Failed in CompareATACBAMs and CompareATAC library metrics, same as Multiome 10k sample; this is due to non-determinism |
nikellepetrillo
approved these changes
Feb 6, 2025
jessicaway
approved these changes
Feb 6, 2025
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staging --> master