ExternalExomeReprocessing_v2.4.9

2.4.9

2021-09-22

• Updated Utilities.wdl task definitions to include a new task that is NOT used in this pipeline.

ExomeReprocessing_v2.4.9

2.4.9

2021-09-22

• Updated Utilities.wdl task definitions to include a new task that is NOT used in this pipeline.

ExomeGermlineSingleSample_v2.4.7

2.4.7

2021-09-22

• Updated Utilities.wdl task definitions to include a new task that is NOT used in this pipeline.

Arrays_v2.4.2

2.4.2

2021-09-22

• Enabled pipeline to lookup the bead_pool_manifest_file using an alternate method (using the arrays_metadata_path and bead_pool_manifest_filename)

ValidateChip_v1.13.3

1.13.3

2021-09-09

• Set the volatile=true flag for several internal tasks so they will not use call-caching

SmartSeq2SingleSample_v5.1.4

5.1.4

2021-09-02 (Date of Last Commit)

• Removed a redundant task in Picard.wdl that was used in a previous pipeline. However,
  that wdl also contains other Picard task that are used in the smartseq2 single sample. Therefore,
  the smartseq2 single sample is not expected to change.

SmartSeq2SingleNucleus_v1.0.2

1.0.2

2021-09-02 (Date of Last Commit)

• Added a new StarSolo task for another pipeline in the StarAlign.wdl. However, the same wdl
  contains other Star tasks that are used in the smartseq2 single nuclei for paired and
  single stranged fastq files. As a result, the smartseq2 processing is not expected to
  change.

Optimus_v5.0.0

5.0.0

2021-08-30 (Date of Last Commit)

• Replaced STAR alignment with STARsolo and modified the structure of the WDL to utilize the UMI and barcode correction from STARsolo. In the new implementation of Optimus, STARsolo uses the FASTQ file as input and directly creates a count matrix file and a BAM file. No updates have been made to the inputs or outputs. The data from this version can be co-analyzed with previous Optimus versions.

MultiSampleSmartSeq2_v2.2.5

2.2.5

2021-09-02 (Date of Last Commit)

• Removed a redundant task in Picard.wdl that was used in a previous pipeline. However,
  that wdl also contains other Picard task that are used in the smartseq2 single sample. Therefore,
  the smartseq2 single sample is not expected to change.

MultiSampleSmartSeq2SingleNucleus_v1.0.3

1.0.3

2021-09-02 (Date of Last Commit)

• Added a new StarSolo task for another pipeline in the StarAlign.wdl. However, the same wdl
  contains other Star tasks that are used in the smartseq2 single nuclei for paired and
  single stranged fastq files. As a result, the smartseq2 processing is not expected to
  change.