6.1.5

2026-02-24 (Date of Last Commit)

Added 2 new outputs to Multiome.wdl: gex_whitelist_used and atac_whitelist_used; these outputs indicate the whitelist used for the gene expression and ATAC pipelines, respectively. This change is provenance-only and introduces no functional changes to pipeline outputs
Added whitelist provenance tracking to JoinMultiomeBarcodes by storing the GEX and ATAC whitelist paths in the h5ad unstructured metadata (.uns). This change is provenance-only and introduces no functional changes to pipeline outputs

6.1.4

2026-01-22 (Date of Last Commit)

Added a new, defaulted input cellbender_memory_GB to Optimus; this does not affect the outputs of this pipeline
Added a task level input, mem_size, to StarSoloFastq to expose memory settings; this does not affect the outputs of this pipeline

6.1.3

2025-08-15 (Date of Last Commit)

Added an option to input an aligned ATAC BAM file to the Multiome pipeline; this allows users to skip the ATAC alignment step if they already have an aligned BAM file

6.1.2

2025-08-06 (Date of Last Commit)

Added MaskPeakCallingMetrics task to remove inappropriate library level peak calling metrics from PairedTag

6.1.1

25-07-31 (Date of Last Commit)

Reorganized all WDL pipelines into the wdl pipeline directory

6.1.0

25-07-16 (Date of Last Commit)

Added reference genome/GTF headers to fragment file via new string inputs

6.0.5

2025-06-18 (Date of Last Commit)

Added the exclude_chroms input parameter to the snap.metrics.tsse function in the CreateFragmentFile task of the ATAC pipeline; which is a list of chromosomes to exclude in per cell metric computation. The default value is [chrM, M]

6.0.4

25-06-06 (Date of Last Commit)

Added mito_list (a list of strings) as an input parameter to CreateFragmentFile task of the ATAC pipeline. This specifies the chromosome names considered mitochondrial DNA. The default value is [chrM, M]
Removed quotes from bootDiskSizeGb in RunEmptyDrops task to be compatible with Google Batch; this does not affect the outputs of the pipeline
Increased the ulimit in the following tasks: CalculateCellMetrics, CalculateGeneMetrics, CalculateUMIsMetrics; this does not affect the outputs of the pipeline

6.0.3

25-05-27 (Date of Last Commit)

Increased the ulimit in the STARsoloFastq task in the StarAlign.wdl to 10000; this does not affect the outputs of the pipeline

6.0.2

25-04-16 (Date of Last Commit)

Added cloud_provider to peakcalling task in Multiome.wdl and fix commit history

6.0.1

25-04-15 (Date of Last Commit)

Refactored peak calling task to be called from PeakCalling.wdl

6.0.0

2025-04-02 (Date of Last Commit)

Implemented a unified STARsolo execution strategy to ensure consistent and accurate cell barcode correction across the entire dataset. This update resolves discrepancies that previously arose from sharded (partitioned) processing, where each shard independently corrected barcodes using incomplete local priors. By consolidating barcode frequency calculations and applying correction globally, the pipeline now mirrors the behavior of DropSeq and Cell Ranger pipelines
Refactored the STAR alignment step (STARsoloFastq) in Optimus and removed tasks FastqProcessing and MergeSortBamFiles
Removed MergeStarOutput tasks from Optimus pipeline; added necessary parts of MergeStarOutput task to the STAR alignment step (STARsoloFastq). Additional outputs added to STARsoloFastq task as a result; this includes row_index, col_index, sparse_counts, library_metrics, mtx_files, filtered_mtx_files and cell_reads_out
Updated the STAR docker image to include Samtools and Python

5.11.0

2025-02-25 (Date of Last Commit)

Refactored the Peak Calling step of Multiome to use the JoinBarcodes output h5ad as the input for peak calling, ensuring the h5ad files have both GEX and ATAC barcodes
Updated the warp-tools docker image to include an update to the GroupQCs function in sctools; this does not affect the outputs of the pipeline
Added reference information to the BAM headers

5.10.0

2025-02-03 (Date of Last Commit)

Added an optional PeakCalling task to the ATAC workflow
Added a boolean variable run_peak_calling to the Multiome pipeline; default is false

5.9.6

2025-01-21 (Date of Last Commit)

Added a boolean variable is_slidetags; default is false but it is set to true if the Slide-Tags pipeline is calling Optimus
Added reference_gtf_file to the output h5ad unstructured metadata
Added the ATAC fragment file CSI index as high-level ATAC workflow output; this does not impact the Multiome workflow as Multiome already produces the csi index from ATAC

5.9.4

2024-12-05 (Date of Last Commit)

Moved the optional CellBender task to the Optimus.wdl

5.9.3

2024-12-3 (Date of Last Commit)

Fixed a bug in the StarSoloFastq task that caused the pipeline to not output a UniqueAndMult-Uniform.mtx when --soloMultiMappers Uniform was passed to STAR

5.9.2

2024-11-22 (Date of Last Commit)

Added bam validation in the StarSoloFastq task; this does not affect the outputs of the pipeline
Updated the warp-tools docker; this update changes the way gene_names are identified when creating gene expression h5ad files

5.9.1

2024-11-12 (Date of Last Commit)

Renamed the ATAC workflow library metric percent_target to atac_percent_target for compatibility with downstream tools
Added more disk and memory to the JoinBarcodes task

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

5.8.0

2024-10-23 (Date of Last Commit)

Updated the workflow to include a new expected_cells input parameter describing the number of cells used as input to the library preparation; this is passed to both the ATAC workflows and Optimus workflows and the default is set to 3000 cells
Updated the ATAC library CSV and the Gene Expression library CSV to be consistent in file naming convention and to have similar case for metric names
Added a new metric to the ATAC library CSV to calculate percent_target, which is the number of estimated cells by SnapATAC2 divided by expected_cells input
Updated the ATAC workflow so that the output fragment file is bgzipped by default
Updated memory settings for PairedTag; does not impact the Multiome workflow

5.7.1

2024-10-18 (Date of Last Commit)

Removed the underscore of the NHashID in the ATAC library metrics CSV to match the gene expression library metrics

5.7.0

2024-09-24 (Date of Last Commit)

Added a python implementation of DoubletFinder to calculate doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
Updated gene_names in the final h5ad to be unique

5.6.1

2024-09-11 (Date of Last Commit)

Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the Multiome pipeline

5.6.0

2024-08-02 (Date of Last Commit)

Updated the SnapATAC2 docker to include v2.7.0; the pipeline will now produce a library-level summary metric CSV for the BAM.

5.5.0

2024-08-06 (Date of Last Commit)

Updated the warp-tools docker to calculate mitochondrial reads from unique reads in cell and gene metrics; these metrics are in the cell and gene metrics CSV as well as h5ad

5.4.1

2024-08-02 (Date of Last Commit)

The ubuntu_16_0_4 docker image version was pinned instead of using the latest tag; this does not affect the outputs of the pipeline

5.4.0

2024-07-25 (Date of Last Commit)

Updated the warp-tools docker image to add TSO metrics to the output h5ad and metric CSV files
Update the library-level metrics to include new TSO metrics and NHashID descriptor

5.3.1

2024-07-18 (Date of Last Commit)

The atac.wdl was refactored into its own directory under the pipelines/wdl directory; this change does not impact the Multiome outputs

5.3.0

2024-07-11 (Date of Last Commit)

Updated the Multiome.wdl to run on Azure; cloud_provider is a new, required input

5.2.0

2024-07-09 (Date of Last Commit)

Added new optional input parameter of nhash_id, an optional identifier for a library aliquot that is echoed in the ATAC fragment h5ad, the gene expression h5ad (in the data.uns), and the gene expression library metrics CSV output; default is set to null
Added test statements again for GH action (to release from develop). Will probably revert

5.1.0

2024-06-28 (Date of Last Commit)

Updated the STARsolo parameters for estimating cells to Emptydrops_CR
Added an optional input for expected cells which is used for metric calculation

5.0.0

2024-05-20 (Date of Last Commit)

Updated SnapATAC2 docker to SnapATAC2 v2.6.3; this impacts the workflow output metrics

4.0.2

2024-05-14 (Date of Last Commit)

Updated the Paired-tag Demultiplex task so that some intermediate input names have been renamed; this change does not impact the Multiome workflow

4.0.1

2024-05-10 (Date of Last Commit)

Updated the Paired-tag Demultiplex task; this change does not impact the Multiome workflow

4.0.0

2024-04-24 (Date of Last Commit)

Updated the input parameters for STARsolo in STARsoloFastq task. These include the parameters: soloCBmatchWLtype, soloUMIdedup and soloUMIfiltering
Added "Uniform" as the default string for STARsolo multimapping parameters

3.4.2

2024-04-03 (Date of Last Commit)

Modified adaptor trimming in Paired-tag WDL; this does not impact Multiome

3.4.1

2024-03-26 (Date of Last Commit)

Updated the median umi per cell metric for STARsolo library-level metrics

3.4.0

2024-03-15 (Date of Last Commit)

Added cell metrics to the library-level metrics
Updated the docker for the MergeStarOutput task to include STARsolo v2.7.11a and custom scripts to create a uniform matrix file and scripts to collect library-level metrics from STARsolo output
Modified the MergeStarOutput to call a custom script for creating a uniform matrix file (mtx) from individual shard mtx files and to create a filtered matrix from the uniform matrix with STARsolo

3.3.0

2024-02-28 (Date of Last Commit)

Added the gene expression library-level metrics CSV as output of the Multiome pipeline; this is produced by the Optimus subworkflow

3.2.1

2024-02-29 (Date of Last Commit)

Moved the disk and mem for the Multiome Join Barcodes task into the task inputs section

3.2.0

2024-02-22 (Date of Last Commit)

Updated StarAlign.MergeStarOutput to add a shard number to the metrics files
Removed ref_genome_fasta input from Multiome WDL and JSON

3.1.3

2024-02-07 (Date of Last Commit)

Updated the Metrics tasks to exclude mitochondrial genes from reads_mapped_uniquely, reads_mapped_multiple and reads_mapped_exonic, reads_mapped_exonic_as and reads_mapped_intergenic

3.1.2

2024-02-01 (Date of Last Commit)

Add new paired-tag task to parse sample barcodes from cell barcodes when preindexing is set to true; this does not affect the Multiome pipeline

3.1.1

2024-01-30 (Date of Last Commit)

Added task GetNumSplits before FastqProcess ATAC task to determine the number of splits based on the bwa-mem2 machine specs
Added an error message to the BWAPairedEndAlignment ATAC task to ensure that the number of splits equal the number of ranks
Added an error message to the BWAPairedEndAlignment ATAC task to ensure that the number of R1s equals to the number of R3s

3.1.0

2024-01-24 (Date of Last Commit)

Promote aligner_metrics from Optimus task level outputs to Multiome pipeline level outputs

3.0.5

2024-01-18 (Date of Last Commit)

Increased memory for MergeStarOutputs in StarAlign.wdl, RunEmptyDrops in RunEmptyDrops.wdl, OptimusH5ad in H5adUtils.wdl and GeneMetrics in Metrics.wdl
Added the --soloMultiMappers flag as an optional input to the StarSoloFastq task in the StarAlign.wdl
Added a check of read2 length to the paired-tag pipeline; this does not affect the Multiome workflow

3.0.4

2024-01-05 (Date of Last Commit)

Added new functionality to the ATAC workflow for paired-tag data, including the option for SnapATAC to pull cell barcodes from the BB tag of the BAM
Modified the STARsoloFastq task in the StarAlign.wdl so STARsolo can run different types of alignments in a single STARsolo command depending on the counting_mode

3.0.3

2023-12-20 (Date of Last Commit)

Added updated docker to BWAPairedEndAlignment ATAC task to use updated code for distributed bwa-mem2 from Intel
Removed MergedBAM ATAC and moved BWAPairedEndAlignment ATAC outside of the for loop
Changed CPU platform to Ice Lake for BWAPairedEndAlignment ATAC task
Added input parameter input_output_parameter to the Multiome ATAC wdl

3.0.2

2023-12-20 (Date of Last Commit)

JoinMultiomeBarcodes now has dynamic memory and disk allocation

3.0.1

2023-12-12 (Date of Last Commit)

ValidateVcfs now has optional memory parameter; this does not affect this pipeline
Downgraded Cell Bender from v0.3.1 to v0.3.0

3.0.0

2023-11-22 (Date of Last Commit)

Added gene expression barcodes to the Multiome ATAC fragment file
Updated the JoinBarcodes task to bgzip and tabix the final ATAC fragment file
Added the tabix index file as an output to Multiome

2.3.3

2023-11-21 (Date of Last Commit)

Added the latest warp-tools docker to tasks in the Metrics, FastqProcessing and H5adUtils wdls; this incorporates new input parameter for number of output fastq files to fastqprocess

2.3.2

2023-11-20 (Date of Last Commit)

Added an optional task to the Multiome.wdl that will run CellBender on the Optimus output h5ad file

2.3.1