3.1.6-3.2.1

• the Sanger WXS variant calling workflow has been converted to be a WFPM-compatible workflow package
• now CI testing is done by GitHub Actions
• added support for local mode in which data and metadata inputs are supplied directly by the user, instead of getting them from SONG/SCORE servers
• added a dependent payload-add-uniform-ids@0.1.1 package to insert uniform IDs (DO/SP/SA) to user-provided SONG payload, a feature needed by the ARGO WGs for their benchmarking work
• added test to cover the above new feature
• switched to use helper-functions@1.0.0 for getting secondary files
• switched to use cleanup-workdir@1.0.0 for cleaning up intermediate files upon workflow completion
• updated payload-gen-variant-calling to 0.3.6.0 with publishDir mode set to copy
• no change to any core algorithms

Note:

1. compatible argo-metadata-schema versions: 0.4.0, 0.5.0
2. requires Nextflow 20.07.1 or higher

sanger-wxs-variant-calling.v3.1.6-3.2.1

• Release sanger-wxs-variant-calling.v3.1.6-3.2.1 (b6bf466)
• Package sanger-wxs-variant-calling.v3.1.6-3.2.1.tar.gz (sha256: 73187a708413721cf3675a9a33c1a8dabffadc3ffde85c30c80a96303ced0462)

sanger-wxs-variant-calling.v3.1.6-3.2.0

• Release sanger-wxs-variant-calling.v3.1.6-3.2.0 (f860e5f)
• Package sanger-wxs-variant-calling.v3.1.6-3.2.0.tar.gz (sha256: 51e13a498a0fe24314a8b869d1d596635a1fd8b92857baf6185be2c44ae58f30)

3.1.6-3-1.3

• update payload-gen-variant-calling which ensures vcf and tbi basename match

Note:

1. compatible argo-metadata-schema versions: 0.4.0
2. requires Nextflow 20.07.1 or higher

3.1.6-3-1.2

• enable DSL2: nextflow.preview.dsl = 2 to nextflow.enable.dsl = 2
• update to SONG/SCORE utils 2.3.0
• update to payload-gen-variant-calling 0.3.3.0

Note:

1. compatible argo-metadata-schema versions: 0.4.0
2. requires Nextflow 20.07.1 or higher

3.1.6-3-1.1

• update payload gen module to include session_id

Note: Note: compatible argo-metadata-schema versions: 0.4.0

3.1.6-3-1.0

Sanger variant calling pipeine for Whole eXome Sequencing data. It calls SNV and small Indels, and the pipeline also produces supplement tarballs.

• Somatic SNVs called by CaVEMan
• Somatic Indels called by Pindle

Specific updates

• added defaults for all params, many are empty map [:], this is useful as documenting the params
• updated to generate-bas.0.2.1.0 to explicitly specify tumour or normal bas file
• updated to latest prep tools for harmonized metadata structure for supplement and QC metrics
• updated to payload-gen-variant-calling.0.2.0.0 to produce harmonized metadata structure

Note: compatible argo-metadata-schema versions: 0.3.0