Staging -> master #1198
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Staging -> master #1198
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* add buildindices overview doc and diagram * Km rnawithumis and ss2 doc updates (#1157) * update rnawithumis overview * Update rna-with-umis.methods.md * Update rna-with-umis.methods.md * update multi-snSS2 readme * Update multi_snss2.methods.md * Update multi_snss2.methods.md * update multi-snSS2 docs * update SS2 overview doc * fix python script link
Added paired-tag wrapper and demultiplexing task
Dev -> Staging
Added option to incorporate BB tag in BAM and use it in SnapATAC2 software.
* update overview docs - update pipeline version numbers in Multiome and Optimus Overview docs * update multi-SS2 overview doc * Update smart-seq2.methods.md * update multi-SS2 methods doc * Update doc_style.md * add paired-tag overview doc * Update website/docs/Pipelines/PairedTag_Pipeline/README.md Co-authored-by: ekiernan <[email protected]> * Apply suggestions from LK doc review Co-authored-by: ekiernan <[email protected]> --------- Co-authored-by: ekiernan <[email protected]>
Jw fix jg plumbing test
* integrate multiple soloFeatures * updating counting_mode definition * logic * count exons is true * count exons is true * fix the logic * count exons false * count exons false * echos * echos * echos * rearrange logic * rearrange * testing * testing * testing * count exons true * switch counting mode order * try running in scrna * clean up * snrna countexons is true * snrna countexons is true * snrna countexons is false * snrna countexons is true * snrna countexons is false * cleaning up * changelogs * changelogs * change cpu_platform to Intel Cascade Lake for sci test input * change cpu_platform to Intel Cascade Lake for sci test input * Update pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md Co-authored-by: ekiernan <[email protected]> * Update pipelines/skylab/multiome/Multiome.changelog.md Co-authored-by: ekiernan <[email protected]> * Update pipelines/skylab/optimus/Optimus.changelog.md Co-authored-by: ekiernan <[email protected]> * Update pipelines/skylab/paired_tag/PairedTag.changelog.md Co-authored-by: ekiernan <[email protected]> * Update pipelines/skylab/slideseq/SlideSeq.changelog.md Co-authored-by: ekiernan <[email protected]> --------- Co-authored-by: Juan Pablo Ramos Barroso <[email protected]> Co-authored-by: ekiernan <[email protected]>
* add summary task * change cpu_platform to Intel Cascade Lake for sci test input * change cpu_platform to Intel Cascade Lake for sci test input * change cpu_platform to Intel Cascade Lake for sci test input * Update VerifyTasks.wdl * Update VerifyTasks.wdl
dev to staging
* add summary task * add multimapper option * update optimus plumbing for ease of testing * add echos * add to test * remove some echoes * make mouse snrna json go back to what is in dev * make mouse snrna json go back to what is in dev * add as outputs * typo * changelogs * changelogs * changelogs * update pipeline docs * optional output * optional output * optional output * optional output * docs * docs * docs * Update website/docs/Pipelines/Optimus_Pipeline/README.md Co-authored-by: Kaylee Mathews <[email protected]> * remove optional input to tests --------- Co-authored-by: kayleemathews <[email protected]> Co-authored-by: Kaylee Mathews <[email protected]>
Updated the CompareTabix task in the Verify tasks
* adding read2 length and barcode orientation check task
Added scatter and preemptibles to snM3C
* add summary task * get a bigger machine * more memory * trying out east1 * go back to central and decrease mem and threads * try different zones * make machine smaller * smaller cpu * smaller cpu * more mem * more mem * 2000 disk * more mem compare bams * more mem compare bams * more mem compare bams * no zones * more mem in comparebams * more mem in comparebams * 725000 * 825000 * 725 * max records 3000000 * max records 3000000 * add logic to fail fast if bams differ in size by 200 mb * Update VerifyTasks.wdl
* rc-2483 * update changelog * Update README.md --------- Co-authored-by: kayleemathews <[email protected]> Co-authored-by: ekiernan <[email protected]>
Removed space from Verify Tabix task
Added a task to parse cell barcodes from sample barcodes
* add summary task * move CondensedSnm3C.wdl out of beta * update batch numbers * add sorting to the compare compressed text files * changelogs and versions * revert batch change * batch change * batch change
* Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update website/docs/Pipelines/snM3C/README.md Co-authored-by: Nikelle Petrillo <[email protected]> * Update README.md * fix num_downstr_bases description * Update README.md --------- Co-authored-by: Nikelle Petrillo <[email protected]>
* add summary task * batch change in test wdl
dev -> staging
* add summary task * change diff from 1mb to 0 mb * make logic more clear
* reblocking changes for BGE reblocking test docker fixing TDR index issue in reblock fix the rest of the bge changes adding bge inputs fixes comment renaming inputs fix * changelogs * trying to fix tests * moving test to scientific * dragen gvcfs have a different file extension * missed one * not sure if this fixes the test because the input file is in a sample map * addressing comments * fixing bge tests * fixing tests * typo * one more * updating to gatk 4.5.0.0 * fixing vesion numbers * missed one update to 4.5.0.0 * update for new version of VETS --------- Co-authored-by: Nikelle Petrillo <[email protected]>
dev -> staging
|
DO NOT SQUASH MERGE!!! |
jessicaway
approved these changes
Feb 6, 2024
|
Exome/WGS reprocessing tests are failing due to a misordering of rows in the crosscheck |
ekiernan
approved these changes
Feb 7, 2024
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