From 6aac6b6f3a4d3740dc7719e2b9e910683d72aaec Mon Sep 17 00:00:00 2001 From: khajoue2 Date: Mon, 21 Oct 2024 14:38:43 -0500 Subject: [PATCH 1/2] Fix: Use CSI instead of TBI indexing in tabix command to support chromosomes larger than 512 Mbp. --- pipelines/skylab/multiome/Multiome.changelog.md | 4 ++++ pipelines/skylab/multiome/Multiome.wdl | 2 +- tasks/skylab/H5adUtils.wdl | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md index 378678f9ba..57bda678d8 100644 --- a/pipelines/skylab/multiome/Multiome.changelog.md +++ b/pipelines/skylab/multiome/Multiome.changelog.md @@ -1,3 +1,7 @@ +# 5.7.2 +2024-10-21 (Date of Last Commit) +* Changed a flag in H5adUtils.wdl to se CSI instead of TBI indexing in tabix command to support chromosomes larger than 512 Mbp. + # 5.7.1 2024-10-18 (Date of Last Commit) diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl index 821e5bead6..4217321610 100644 --- a/pipelines/skylab/multiome/Multiome.wdl +++ b/pipelines/skylab/multiome/Multiome.wdl @@ -9,7 +9,7 @@ import "../../../tasks/broad/Utilities.wdl" as utils workflow Multiome { - String pipeline_version = "5.7.1" + String pipeline_version = "5.7.2" input { diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl index 0ac5a3dd66..6eccd67f9c 100644 --- a/tasks/skylab/H5adUtils.wdl +++ b/tasks/skylab/H5adUtils.wdl @@ -317,7 +317,7 @@ task JoinMultiomeBarcodes { echo "Starting bgzip" bgzip "~{atac_fragment_base}.sorted.tsv" echo "Starting tabix" - tabix -s 1 -b 2 -e 3 "~{atac_fragment_base}.sorted.tsv.gz" + tabix -s 1 -b 2 -e 3 -C "~{atac_fragment_base}.sorted.tsv.gz" >>> From 003c7cd276fcf0c8a79f566b5f635bf5d79d9548 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 21 Oct 2024 19:40:15 +0000 Subject: [PATCH 2/2] Updated pipeline_versions.txt with all pipeline version information --- pipeline_versions.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 66a514f5a9..18cad237fa 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -30,7 +30,7 @@ ExomeReprocessing 3.3.1 2024-09-17 BuildIndices 3.0.0 2023-12-06 scATAC 1.3.2 2023-08-03 snm3C 4.0.4 2024-08-06 -Multiome 5.7.1 2024-10-18 +Multiome 5.7.2 2024-10-21 PairedTag 1.7.1 2024-10-18 MultiSampleSmartSeq2 2.2.22 2024-09-11 MultiSampleSmartSeq2SingleNucleus 2.0.1 2024-09-24