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Fix join barcode step for Opossum #1397

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Fix join barcode step for Opossum #1397

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6aac6b6
Fix: Use CSI instead of TBI indexing in tabix command to support chro…
khajoue2 Oct 21, 2024
003c7cd
Updated pipeline_versions.txt with all pipeline version information
actions-user Oct 21, 2024
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2 changes: 1 addition & 1 deletion pipeline_versions.txt
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Expand Up @@ -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
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4 changes: 4 additions & 0 deletions pipelines/skylab/multiome/Multiome.changelog.md
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@@ -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.
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Suggested change
* Changed a flag in H5adUtils.wdl to se CSI instead of TBI indexing in tabix command to support chromosomes larger than 512 Mbp.
* Changed a flag in H5adUtils.wdl to set 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)

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2 changes: 1 addition & 1 deletion pipelines/skylab/multiome/Multiome.wdl
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Expand Up @@ -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 {
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2 changes: 1 addition & 1 deletion tasks/skylab/H5adUtils.wdl
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Expand Up @@ -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"
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@khajoue2 Do we know if this is still compatible with ArchR import? We only added tabix in to make the outputs compatible, so if it isn't directly compatible, we might want to flag it to Multiome group.

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This information wasn't clearly specified in ArchR's public documentation, we can do some downstream check.

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We can make a note "If incompatible, explore alternative solutions e.g., chromosome splitting."


>>>

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