Recent Releases of https://github.com/broadinstitute/warp
https://github.com/broadinstitute/warp - Add optional pipeline header line input variable
- WDL
Published by jsotobroad 10 months ago
https://github.com/broadinstitute/warp - Imputation_develop
1.1.21
2025-09-03 (Date of Last Commit)
- Update UpdateHeader task to add an optional pipelineheaderline input that when supplied, will add a header line containing this value to the header of the output vcf. Currently not used by this pipeline
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ImputationBeagle_develop
2.0.2
2025-09-03 (Date of Last Commit)
- Add optional pipelineheaderline input that when supplied, will add a header line containing this value to the header of the output vcf
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ArrayImputationQuotaConsumed_develop
1.0.5
2025-09-03 (Date of Last Commit)
- Add optional pipelineheaderline input to match beagle imputation pipeline inputs
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ArrayImputationQC_develop
1.0.2
2025-09-03 (Date of Last Commit)
- Add optional pipelineheaderline input to match beagle imputation pipeline inputs
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - local testing of beagle release process
- WDL
Published by jsotobroad 10 months ago
https://github.com/broadinstitute/warp - Array Imputation OOM and FailQCNChunks fixes
- WDL
Published by jsotobroad 10 months ago
https://github.com/broadinstitute/warp - Imputation_develop
1.1.20
2025-08-26 (Date of Last Commit)
- Update tasks to use maxRetries of 1 instead of 2. 1 retry is sufficient for transient errors and helps reduce costs.
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ImputationBeagle_develop
2.0.1
2025-08-26 (Date of Last Commit)
- Update tasks to use maxRetries of 1 instead of 2. 1 retry is sufficient for transient errors and helps reduce costs.
- Split the two nested scatters from each other so no shard will perform phasing/imputation if any shard fails qc checks
- updated phase/impute tasks to work with the retry with more memory workflow option to help with OOM issues we're seeing in those tasks
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ArrayImputationQuotaConsumed_develop
1.0.4
2025-08-26 (Date of Last Commit)
- Update tasks to use maxRetries of 1 instead of 2. 1 retry is sufficient for transient errors and helps reduce costs.
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ArrayImputationQC_develop
1.0.1
2025-08-26 (Date of Last Commit)
- Update tasks to use maxRetries of 1 instead of 2. 1 retry is sufficient for transient errors and helps reduce costs.
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - BuildIndices_v4.1.0
4.1.0
2025-08-20 (Date of Last Commit)
- Added the SNSS2AddIntronsToGTF task to modify human and mouse GENCODE GTF files by adding introns. This is a new output of the pipeline
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - PairedTag_v2.1.8
2.1.8
2025-08-15 (Date of Last Commit)
- Added an option to input an aligned ATAC BAM file to the PairedTag pipeline; this allows users to skip the ATAC alignment step if they already have an aligned BAM file
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - atac_v2.9.2
2.9.2
2025-08-15 (Date of Last Commit)
- Added an option to input an aligned ATAC BAM file; this allows users to skip the ATAC alignment step if they already have an aligned BAM file
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - Multiome_v6.1.3
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
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - ArrayImputationQC_v1.0.0
1.0.0
2025-08-11 (Date of Last Commit)
- Initial release of pipeline to perform QC checks on inputs of the Imputation Beagle pipeline.
- Checks include:
- Called against HG38 reference genome
- VCF version 4.x
- All chromosomes are present
- Not a whole genome sequencing (WGS) file
- WDL
Published by github-actions[bot] 10 months ago
https://github.com/broadinstitute/warp - BuildIndices_develop
4.1.0
2025-08-20 (Date of Last Commit)
- Added the SNSS2AddIntronsToGTF task to modify human and mouse GENCODE GTF files by adding introns. This is a new output of the pipeline
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - atac_develop
2.9.2
2025-08-15 (Date of Last Commit)
- Added an option to input an aligned ATAC BAM file; this allows users to skip the ATAC alignment step if they already have an aligned BAM file
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Multiome_develop
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
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.8
2025-08-15 (Date of Last Commit)
- Added an option to input an aligned ATAC BAM file to the PairedTag pipeline; this allows users to skip the ATAC alignment step if they already have an aligned BAM file
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - ArrayImputationQC_develop
1.0.0
2025-08-11 (Date of Last Commit)
- Initial release of pipeline to perform QC checks on inputs of the Imputation Beagle pipeline.
- Checks include:
- Called against HG38 reference genome
- VCF version 4.x
- All chromosomes are present
- Not a whole genome sequencing (WGS) file
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - MultiSampleSmartSeq2SingleNucleus_v2.2.2
2.2.2
2025-06-20 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - atac_v2.9.1
2.9.1
2025-08-06 (Date of Last Commit)
- Added MaskPeakCallingMetrics task to remove innappropriate peak calling metrics from PairedTag
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - SlideTags_v1.0.2
1.0.2
2025-07-31 (Date of Last Commit)
- Added a new optional input parameter, cellbenderhardwarememory_GB, to the CellBender tasks in the Optimus.wdl; this allows users to specify the hardware memory in GB for the CellBender tasks. The default value is set to 32 GB.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Multiome_v6.1.2
6.1.2
2025-08-06 (Date of Last Commit)
- Added MaskPeakCallingMetrics task to remove innappropriate library level peak calling metrics from PairedTag
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - snm3C_v4.1.0
4.1.0
2025-08-11 (Date of Last Commit)
- Changed read threshold max from 10M to 6M in demulitiplexing step
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - PairedTag_v2.1.7
2.1.7
2025-08-06 (Date of Last Commit)
- Added MaskPeakCallingMetrics task to remove innappropriate library level peak calling metrics from PairedTag
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - SlideSeq_v3.6.3
3.6.3
2025-06-20 (Date of Last Commit) * Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Optimus_v8.0.4
8.0.4
2025-07-31 (Date of Last Commit)
- Added a new optional input parameter, cellbenderhardwarememory_GB, to the CellBender tasks in the Optimus.wdl; this allows users to specify the hardware memory in GB for the CellBender tasks. The default value is set to 32 GB.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - ImputationBeagle_v2.0.0
2.0.0
2025-07-31 (Date of Last Commit)
Breaking changes
- Update ImputationBeagle pipeline to split by chunks of samples to help scale the workflow to more samples. This also includes tasks to split the input VCF into sample chunks, run the imputation on each chunk, and then merge the results back together. These changes change the scientific output of the pipeline.
- Removed SeparateMultiallelics and RemoveSymbolicAlleles tasks as they are not something we want to do anymore.
Additional changes
- Use SSD for tasks that localize large files to help with performance on Google Batch.
- Add maxRetries to all tasks to help with performance on Google Batch.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - ArrayImputationQuotaConsumed_v1.0.3
1.0.3
2025-07-31 (Date of Last Commit)
- Add maxRetries to tasks to help with performance on Google Batch.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Imputation_v1.1.19
1.1.19
2025-07-31 (Date of Last Commit)
- Add maxRetries to tasks to help with performance on Google Batch.
- Use SSD for tasks that localize large files to help with performance on Google Batch.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - snm3C_develop
4.1.0
2025-08-11 (Date of Last Commit)
- Changed read threshold max from 10M to 6M in demulitiplexing step
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - atac_develop
2.9.1
2025-08-06 (Date of Last Commit)
- Added MaskPeakCallingMetrics task to remove innappropriate peak calling metrics from PairedTag
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Multiome_develop
6.1.2
2025-08-06 (Date of Last Commit)
- Added MaskPeakCallingMetrics task to remove innappropriate library level peak calling metrics from PairedTag
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.7
2025-08-06 (Date of Last Commit)
- Added MaskPeakCallingMetrics task to remove innappropriate library level peak calling metrics from PairedTag
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - ImputationBeagle_develop
2.0.0
2025-07-31 (Date of Last Commit)
Breaking changes
- Update ImputationBeagle pipeline to split by chunks of samples to help scale the workflow to more samples. This also includes tasks to split the input VCF into sample chunks, run the imputation on each chunk, and then merge the results back together. These changes change the scientific output of the pipeline.
- Removed SeparateMultiallelics and RemoveSymbolicAlleles tasks as they are not something we want to do anymore.
Additional changes
- Use SSD for tasks that localize large files to help with performance on Google Batch.
- Add maxRetries to all tasks to help with performance on Google Batch.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - ArrayImputationQuotaConsumed_develop
1.0.3
2025-07-31 (Date of Last Commit)
- Add maxRetries to tasks to help with performance on Google Batch.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Imputation_develop
1.1.19
2025-07-31 (Date of Last Commit)
- Add maxRetries to tasks to help with performance on Google Batch.
- Use SSD for tasks that localize large files to help with performance on Google Batch.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - SlideTags_develop
1.0.2
2025-07-31 (Date of Last Commit)
- Added a new optional input parameter, cellbenderhardwarememory_GB, to the CellBender tasks in the Optimus.wdl; this allows users to specify the hardware memory in GB for the CellBender tasks. The default value is set to 32 GB.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.6
2025-07-31 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Multiome_develop
6.1.1
25-07-31 (Date of Last Commit)
- Added a new optional input parameter, cellbenderhardwarememory_GB, to the CellBender tasks in the Optimus.wdl; this allows users to specify the hardware memory in GB for the CellBender tasks. The default value is set to 32 GB.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - Optimus_develop
8.0.4
2025-07-31 (Date of Last Commit)
- Added a new optional input parameter, cellbenderhardwarememory_GB, to the CellBender tasks in the Optimus.wdl; this allows users to specify the hardware memory in GB for the CellBender tasks. The default value is set to 32 GB.
- WDL
Published by github-actions[bot] 11 months ago
https://github.com/broadinstitute/warp - SlideSeq_develop
3.6.3
2025-06-20 (Date of Last Commit) * Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 12 months ago
https://github.com/broadinstitute/warp - SlideTags_develop
1.0.1
2025-06-20 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 12 months ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.5
2025-07-16 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 12 months ago
https://github.com/broadinstitute/warp - MultiSampleSmartSeq2SingleNucleus_develop
2.2.2
2025-06-20 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 12 months ago
https://github.com/broadinstitute/warp - Multiome_develop
6.1.0
25-07-16 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs
- WDL
Published by github-actions[bot] 12 months ago
https://github.com/broadinstitute/warp - Optimus_develop
8.0.3
2025-06-20 (Date of Last Commit)
- Added reference genome/GTF headers to fragment file via new string inputs; this change does not affect this pipeline
- WDL
Published by github-actions[bot] 12 months ago
https://github.com/broadinstitute/warp - PairedTag_v2.1.4
2.1.4
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]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_v6.0.5
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]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - atac_v2.9.0
2.9.0
2025-06-18 (Date of Last Commit)
- Added the exclude_chroms input parameter to the snap.metrics.tsse function in the CreateFragmentFile task; which is a list of chromosomes to exclude in per cell metric computation. The default value is [chrM, M]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.4
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]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_develop
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]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - atac_develop
2.9.0
2025-06-18 (Date of Last Commit)
- Added the exclude_chroms input parameter to the snap.metrics.tsse function in the CreateFragmentFile task; which is a list of chromosomes to exclude in per cell metric computation. The default value is [chrM, M]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - snm3C_v4.0.5
4.0.5
2025-06-16 (Date of Last Commit)
- Switched the cromwellrootdir variable to be compatabile with Google Batch
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - snm3C_develop
4.0.5
2025-06-16 (Date of Last Commit)
- Switched the cromwellrootdir variable to be compatabile with Google Batch
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - MultiSampleSmartSeq2SingleNucleus_v2.2.1
2.2.1
2025-05-27 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Optimus_v8.0.2
8.0.2
2025-06-09 (Date of Last Commit)
- 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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideSeq_v3.6.2
3.6.2
2025-06-09 (Date of Last Commit) * Increased the ulimit in the following tasks: CalculateCellMetrics, CalculateGeneMetrics, CalculateUMIsMetrics; this does not affect the outputs of the pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PairedTag_v2.1.3
2.1.3
2025-06-06 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_v6.0.4
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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - MultiSampleSmartSeq2SingleNucleus_develop
2.2.1
2025-05-27 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Optimus_develop
8.0.2
2025-06-09 (Date of Last Commit)
- 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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideSeq_develop
3.6.2
2025-06-09 (Date of Last Commit) * Increased the ulimit in the following tasks: CalculateCellMetrics, CalculateGeneMetrics, CalculateUMIsMetrics; this does not affect the outputs of the pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.3
2025-06-06 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_develop
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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideTags_develop
1.0.0
2025-06-12 (Date of Last Commit)
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - atac_v2.8.0
2.8.0
2025-06-06 (Date of Last Commit)
- Added mito_list (a list of strings) as an input parameter to CreateFragmentFile task. This specifies the chromosome names considered mitochondrial DNA. The default value is [chrM, M]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - atac_develop
2.8.0
2025-06-06 (Date of Last Commit)
- Added mito_list (a list of strings) as an input parameter to CreateFragmentFile task. This specifies the chromosome names considered mitochondrial DNA. The default value is [chrM, M]
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideTags_v1.0.0
1.0.0
2025-06-12 (Date of Last Commit)
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - rnaseq_aou_v9.0.1
rnaseqaouv9.0.1
- WDL
Published by ekiernan about 1 year ago
https://github.com/broadinstitute/warp - SlideTags_develop
1.0.0
2025-06-12 (Date of Last Commit)
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideTags_develop
1.0.0
2025-06-02 (Date of Last Commit)
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.2
2025-05-27 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Optimus_develop
8.0.1
2025-05-27 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_develop
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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideSeq_develop
3.6.1
2025-05-27 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - MultiSampleSmartSeq2SingleNucleus_develop
2.2.1
2025-05-27 (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
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_develop
6.0.2
25-04-16 (Date of Last Commit)
- Added cloud_provider to peakcalling task in Multiome.wdl and fix commit history
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_develop
6.1.1
025-04-15 (Date of Last Commit)
- Refactored peak calling task to be called from PeakCalling.wdl
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - atac_develop
2.7.2
2025-04-15 (Date of Last Commit)
- Refactored peak calling task to be called from PeakCalling.wdl
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PairedTag_develop
2.1.1
2025-04-15 (Date of Last Commit)
- Refactored peak calling task to be called from PeakCalling.wdl
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Multiome_v6.0.0
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 rowindex, colindex, sparsecounts, librarymetrics, mtxfiles, filteredmtxfiles and cellreads_out
- Updated the STAR docker image to include Samtools and Python
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Optimus_v8.0.0
8.0.0
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
- Removed boolean variable is_slidetags; no longer needed with new updates
- Refactored the STAR alignment step and removed tasks FastqProcessing and MergeSortBamFiles
- Added parameters for STARsoloFastq task, including cpuplatformstar, memsizestar, cpustar, diskstar, limitBAMsortRAMstar, and outBAMsortingBinsNstar, for dynamic allocation of resources depending on input size
- Removed MergeStarOutput tasks; added necessary parts of MergeStarOutput task to the STAR alignment step (STARsoloFastq). Additional outputs added to STARsoloFastq task as a result; this includes rowindex, colindex, sparsecounts, librarymetrics, mtxfiles, filteredmtxfiles and cellreads_out
- Updated the STAR docker image to include Samtools and Python
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - MultiSampleSmartSeq2SingleNucleus_v2.2.0
2.2.0
2025-04-02 (Date of Last Commit)
- Removed MergeStarOutput task and updated docker image in alignemnt step (STARsoloFastq) in Optimus; this does not affect the outputs of the pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PairedTag_v2.0.0
2.0.0
2025-04-02 (Date of Last Commit) * Refactored the STAR alignment step in Optimus and removed tasks FastqProcessing and MergeSortBamFiles; we are no longer sharding. We are now running one instance of STAR * 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 rowindex, colindex, sparsecounts, librarymetrics, mtxfiles, filteredmtxfiles and cellreads_out * Updated the STAR docker image to include Samtools and Python
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - PeakCalling_v1.0.0
1.0.0
2025-03-24 (Date of Last Commit)
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - SlideSeq_v3.6.0
3.6.0
2025-04-02 (Date of Last Commit) * Removed MergeStarOutput task and updated docker image in alignemnt step (STARsoloFastq) in Optimus; this does not affect the outputs of the pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - ReblockGVCF_v2.4.1
2.4.1
2025-02-21 (Date of Last Commit)
- Updated HaplotypeCallerGATK4VCF to use MEMSIZE and MEMUNIT; this does not affect the outputs of this pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - VariantCalling_v2.2.5
2.2.5
2025-02-21 (Date of Last Commit)
- Updated HaplotypeCallerGATK4VCF to use MEMSIZE and MEMUNIT; this does not affect the outputs of this pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - ExomeGermlineSingleSample_v3.2.4
3.2.4
2025-02-21 (Date of Last Commit)
- Updated HaplotypeCallerGATK4VCF to use MEMSIZE and MEMUNIT; this does not affect the outputs of this pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - WholeGenomeGermlineSingleSample_v3.3.4
3.3.4
2025-02-12 (Date of Last Commit)
- Updated HaplotypeCallerGATK4VCF to use MEMSIZE and MEMUNIT; this does not affect the outputs of this pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - UltimaGenomicsWholeGenomeGermline_v1.2.0
1.2.0
2025-03-17 (Date of Last Commit)
- Updated Picard docker for CompareMetrics from 2.20.4-SNAPSHOT to 2.26.10-SNAPSHOT to fix security vulnerability. The outputs of the CollectAggregationMetrics task have changed slightly: .alignmentsummarymetrics now have additional columns SDREADLENGTH, MEDIANREADLENGTH, MADREADLENGTH, MINREADLENGTH, MAXREADLENGTREADSALIGNEDINPAIRS, PCTSOFTCLIP, PCTHARDCLIP, AVGPOS3PRIMESOFTCLIPLENGTH. Additionally, a histogram is now included in the .alignmentsummary_metrics file
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - UltimaGenomicsWholeGenomeCramOnly_v1.1.0
1.1.0
2025-03-17 (Date of Last Commit)
- Updated Picard docker for CompareMetrics from 2.20.4-SNAPSHOT to 2.26.10-SNAPSHOT to fix security vulnerability. The outputs of the CollectAggregationMetrics task have changed slightly: .alignmentsummarymetrics now have additional columns SDREADLENGTH, MEDIANREADLENGTH, MADREADLENGTH, MINREADLENGTH, MAXREADLENGTREADSALIGNEDINPAIRS, PCTSOFTCLIP, PCTHARDCLIP, AVGPOS3PRIMESOFTCLIPLENGTH. Additionally, a histogram is now included in the .alignmentsummary_metrics file
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - ExomeReprocessing_v3.3.4
3.3.4
2025-02-21 (Date of Last Commit)
- Updated HaplotypeCallerGATK4VCF to use MEMSIZE and MEMUNIT; this does not affect the outputs of this pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - WholeGenomeReprocessing_v3.3.4
3.3.4
2025-02-21 (Date of Last Commit)
- Updated HaplotypeCallerGATK4VCF to use MEMSIZE and MEMUNIT; this does not affect the outputs of this pipeline
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - Imputation_v1.1.18
1.1.18
2025-04-07 (Date of Last Commit)
- Update Imputation Tasks to not request external IP addresses (use runtime attribute 'noAddress: true').
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - ImputationBeagle_v1.0.2
1.0.2
2025-04-07 (Date of Last Commit)
- Update Imputation Tasks to not request external IP addresses (use runtime attribute 'noAddress: true').
- WDL
Published by github-actions[bot] about 1 year ago
https://github.com/broadinstitute/warp - ArrayImputationQuotaConsumed_v1.0.2
1.0.2
2025-04-07 (Date of Last Commit)
- Update Imputation Tasks to not request external IP addresses (use runtime attribute 'noAddress: true').
- WDL
Published by github-actions[bot] about 1 year ago