PD-2483 #1182
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PD-2483 #1182
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Can one of the admins verify this patch? |
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Can one of the admins verify this patch? |
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Remember to squash merge! |
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Remember to squash merge! |
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@rsc3 This will require some minor documentation updates. I can take a look and make those updates today! |
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Remember to squash merge! |
kayleemathews
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Jan 24, 2024
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nikellepetrillo
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Feb 5, 2024
* update paths to input files * update jg sample map * Km buildindices docs (#1158) * 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 * Lk pd2448 upstools (#1150) Added paired-tag wrapper and demultiplexing task * PD-2435 Test bwa-mem2 step and run Intel distributed BWA-MEM2 (#1147) * Lk pd2453 add bb tag (#1161) Added option to incorporate BB tag in BAM and use it in SnapATAC2 software. * km paired-tag docs (#1165) * 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 <55763654+ekiernan@users.noreply.github.com> * Apply suggestions from LK doc review Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> --------- Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> * Np jprb pd 2353 multiple star rsolo align (#1164) * 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 <55763654+ekiernan@users.noreply.github.com> * Update pipelines/skylab/multiome/Multiome.changelog.md Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> * Update pipelines/skylab/optimus/Optimus.changelog.md Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> * Update pipelines/skylab/paired_tag/PairedTag.changelog.md Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> * Update pipelines/skylab/slideseq/SlideSeq.changelog.md Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> --------- Co-authored-by: Juan Pablo Ramos Barroso <jpramosbarroso@gmail.com> Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> * Np update multiome sci test (#1167) * 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 * PD-2422 BICAN_Optimus_2nymxis_Oct_2023 (#1152) * Np multimapper param starsolo (#1172) * 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 <95316074+kayleemathews@users.noreply.github.com> * remove optional input to tests --------- Co-authored-by: kayleemathews <kmathews@broadinstitute.org> Co-authored-by: Kaylee Mathews <95316074+kayleemathews@users.noreply.github.com> * added exit code to CompareTabix (#1174) Updated the CompareTabix task in the Verify tasks * Lk pd 2452 add read length check (#1171) * adding read2 length and barcode orientation check task * Lk pd 2464 batch methylome (#1181) Added scatter and preemptibles to snM3C * Np edit resources needed for bwa task / add logic to compareBams (#1183) * 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 * PD-2483 (#1182) * rc-2483 * update changelog * Update README.md --------- Co-authored-by: kayleemathews <kmathews@broadinstitute.org> Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> * PD-2476: Add task before fastqprocess to find number of splits (#1178) * removed space (#1184) Removed space from Verify Tabix task * Lk pd 2455 pairedtag parsebarcodes (#1186) Added a task to parse cell barcodes from sample barcodes * Np move snm3c from beta pipelines (#1185) * 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 * Km snm3c overview doc (#1179) * 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 <38223776+nikellepetrillo@users.noreply.github.com> * Update README.md * fix num_downstr_bases description * Update README.md --------- Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com> * Np fix snm3c test (#1190) * add summary task * batch change in test wdl --------- Co-authored-by: Kaylee Mathews <95316074+kayleemathews@users.noreply.github.com> Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> Co-authored-by: aawdeh <awdeh@broadinstitute.org> Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com> Co-authored-by: Juan Pablo Ramos Barroso <jpramosbarroso@gmail.com> Co-authored-by: kayleemathews <kmathews@broadinstitute.org> Co-authored-by: Robert Sidney Cox III <sidcox@broadinstitute.org>
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Description
Update Multiome metrics with aligner_metrics from Optimus
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Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.