Fix join barcode step for Opossum

[khajoue2]

Fix tabix indexing for large chromosomes

Issue

The previous tabix command was failing due to limitations in TBI (tabix) index
format when dealing with large chromosomes (>512 Mbp). The error message was:

"Region 536870658..536870963 cannot be stored in a tbi index. Try using a csi index"

Fix

Modified the tabix command to use CSI (Coordinate-Sorted Index) instead of TBI.
CSI can handle much larger chromosome sizes.

Changed from:
tabix -s 1 -b 2 -e 3 "${atac_fragment_base}.sorted.tsv.gz"

To:
tabix -s 1 -b 2 -e 3 -C "${atac_fragment_base}.sorted.tsv.gz"

The -C flag tells tabix to create a CSI index. This allows indexing of larger
genomic regions while maintaining the specific column structure of our file.

Impact

This change allows successful indexing of ATAC fragment files that contain
genomic regions larger than 512 Mbp, improving compatibility with a wider
range of reference genomes and ensuring the pipeline can handle larger
chromosomes without failing at the indexing step.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
PairedTag.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

[ekiernan]

@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.

[khajoue2]

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

[khajoue2]

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

[ekiernan]

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.