Optimus_v4.1.2

4.1.2

2020-10-13 (Date of Last Commit)

• Added a new docker in LoomUtils.wdl

MultiSampleSmartSeq2_v2.1.2

2.1.2

2020-10-13 (Date of Last Commit)

• Fixed a bug in the loom file generation script that appeared when using optional input input_id_metadata_field
• Updated the docker in LoomUtils.wdl task to v0.0.3

ValidateChip_v1.12.0

1.12.0

2020-10-07

• Updated task definitions to include a new tool not currently used in ValidateChip wdl
• Updated all internal tasks to use the latest version of picard-private as best practice.

SmartSeq2SingleSample_v5.0.1

5.0.1

2020-10-01 (Date of Last Commit)

• Added check to see if input fastq files are compressed in HISAT2.wdl task

Optimus_v4.1.1

4.1.1

2020-10-07 (Date of Last Commit)

• Removed extra trailing slash in ouput directory from cloud to cloud copy job

• Removed fastq_suffix optional input - the pipeline now dynamically determines if a file is zipped

MultiSampleSmartSeq2_v2.1.1

2.1.1

2020-10-01 (Date of Last Commit)

• Added checks for compressed fastq input files

Arrays_v2.3.0

2.3.0

2020-10-07

• Added use of BafRegress to the pipeline. BafRegress detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.
• Updated all internal tasks to use the latest version of picard-private as best practice.

WholeGenomeGermlineSingleSample_v2.1.0

2.1.0

2020-08-18

• Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52

ValidateChip_v1.11.0

1.11.0

2020-10-01

• Updated task definitions to include a new tool not currently used in ValidateChip wdl

Optimus_v4.1.0

4.1.0

2020-10-05 (Date of Last Commit)

• Updated sctools dockers and made them consistent across the Optimus pipeline