UltimaGenomicsWholeGenomeCramOnly_v1.0.23

1.0.23

2024-11-04 (Date of Last Commit)

• Updated to GATK version 4.6.1.0

UltimaGenomicsJointGenotyping_v1.2.2

1.2.2

2024-11-04 (Date of Last Commit)

• Updated to GATK version 4.6.1.0

SlideSeq_v3.4.4

3.4.4

2024-11-04 (Date of Last Commit)

• Updated the tabix flag in JoinMultiomeBarcodes task in H5adUtils.wdl to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp; this task should not affect the Slide-seq pipeline

ReblockGVCF_v2.3.2

2.3.2

2024-11-04 (Date of Last Commit)

• Updated to GATK version 4.6.1.0

RNAWithUMIsPipeline_v1.0.18

1.0.18

2024-11-04 (Date of Last Commit)

• Updated to GATK version 4.6.1.0

PairedTag_v1.8.1

1.8.1

2024-11-04 (Date of Last Commit)

• Updated the tabix flag in JoinMultiomeBarcodes task in H5adUtils.wdl to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp; this task should not affect the Paired-Tag pipeline

Optimus_v7.8.1

7.8.1

2024-11-04 (Date of Last Commit)

• Updated the tabix flag in JoinMultiomeBarcodes task in H5adUtils.wdl to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp; this task should not affect the Optimus pipeline

Multiome_v5.9.0

5.9.0

2024-10-21 (Date of Last Commit)

• Updated the tabix flag in JoinMultiomeBarcodes task in H5adUtils.wdl to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp; this task changes the format for the ATAC fragment file index
• Renamed the fragment file index from atac_fragment_tsv_tbi to atac_fragment_tsv_index

MultiSampleSmartSeq2SingleNucleus_v2.0.3

2.0.3

2024-11-04 (Date of Last Commit)

• Updated the tabix flag in JoinMultiomeBarcodes task in H5adUtils.wdl to use CSI instead of TBI indexing, which supports chromosomes larger than 512 Mbp; this task should not affect the snSS2 pipeline

JointGenotyping_v1.7.2

1.7.2

2024-11-04 (Date of Last Commit)

• Updated to GATK version 4.6.1.0