Update Loom_schema.md #1080
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Update Loom_schema.md #1080
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khajoue2
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Nov 2, 2023
* Update Loom_schema.md (#1080) * Lk dynamically select barcode orientation (#1086) * Added dynamic barcode selection to the ATAC FastqProcess task * Np pd 2327 separate unmapped reads (#1084) * add separate unmapped reads task * clean up * add splut unmapped reads (#1087) * KM Update metrics descriptions (#1088) * Update metrics descriptions * Update Loom_schema.md * Update Loom_schema.md * Add TagSort and definitions * Km fix broken links in docs (#1090) * Update Terra link address * Fix links to snaptools Docker * Fixed link to SS2 overview * Update link to snM3C test_inputs directory * Fixed link to Multiome test data * Fix link to loom_to_h5ad.py script * Fix link to loom creation script * Fixed links * Lk pd 2363 join barcodes (#1089) Added GEX and ATAC whitelist barcodes to both ATAC and GEX h5ad files so that barcodes that can be joined. * Update UnmappedBamToAlignedBam.wdl (#1070) Changed MarkDuplicates task to use Float size(Array[File], [String]) * Np add single end r1 r2 mapping dna mode and merge sort split reads by name (#1092) * echo whitelistnew task * rearranging * cleaning up * cleaning up * cleaning up * formatting --------- Co-authored-by: aawdeh <[email protected]> * Lk pd 2374 update whitelist (#1093) Updated path of multiome whitelists * Km fix broken links in WARP docs (#1097) * Update Multiome README * Update broken links in docs * Update get-started.md * Update broken bookmarks in docs * Remove the dropna and MATCH columns from JoinBarcodes (#1098) * Remove the dropna and MATCH columns from JoinBarcodes * PD-2379-add_remove_overlap_read_parts_task (#1094) * Added merge_original_and_split_bam_sort_all_reads_name_and_position * Cleaning up a few ls and pwds, adding echos * add task dedup_unique_bam_and_index_unique_bam (#1103) * Km atac h5ad overview (#1102) * Create count-matrix-overview.md * Update count-matrix-overview.md * Add barcode column names Add the column names containing the GEX and ATAC barcodes in the output h5ad files to the Multiome README * Update count-matrix-overview.md * Update README.md * Km doc updates (#1100) * Update links in Optimus Overview doc * Update version numbers in READMEs * Update count-matrix-overview.md * Update count-matrix-overview.md * Add link to SnapATAC2 import_data function * Update count-matrix-overview.md * Update website/docs/Pipelines/ATAC/count-matrix-overview.md Co-authored-by: ekiernan <[email protected]> * Update website/docs/Pipelines/ATAC/count-matrix-overview.md Co-authored-by: ekiernan <[email protected]> * Update website/docs/Pipelines/ATAC/count-matrix-overview.md Co-authored-by: ekiernan <[email protected]> --------- Co-authored-by: ekiernan <[email protected]> * Add unique_reads_allc * Update CondensedSnm3C.wdl * Km add atac rrid and update multiome readme (#1109) * Update Multiome README * Update pipeline version output * Update README.md * Update inputs to CramToUnmappedBam test (#1104) * update paths to input files * Add unique_reads_cgn_extraction task (#1107) --------- Co-authored-by: ekiernan <[email protected]> Co-authored-by: Nikelle Petrillo <[email protected]> Co-authored-by: Kaylee Mathews <[email protected]> Co-authored-by: aawdeh <[email protected]> Co-authored-by: ekiernan <[email protected]> Co-authored-by: Jessica Way <[email protected]>
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Description
This PR is to fix the issues with the Optimus metric definitions raised in #1079
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.