2.1.0-9.3.0

• switched to use song-score-download@2.6.1 that supports retry on song/score temporary failures
• switched to use song-score-upload@2.6.1 that supports retry on song/score temporary failures

Note:

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

sanger-wgs-variant-calling.v2.1.0-9.3.0

• Release sanger-wgs-variant-calling.v2.1.0-9.3.0 (1e95adb)
• Package sanger-wgs-variant-calling.v2.1.0-9.3.0.tar.gz (sha256: be9fdfb371cd15fb7779e43a2a7792230b54a252b4a652ee2bc6be24428bc8af)

2.1.0-9.2.0

• the Sanger WGS 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-wgs-variant-calling.v2.1.0-9.2.0

• Release sanger-wgs-variant-calling.v2.1.0-9.2.0 (fda1871)
• Package sanger-wgs-variant-calling.v2.1.0-9.2.0.tar.gz (sha256: 4c803ef02f2901a1f6a107808806242492d2d7cc5333b9d494b35a3c0cd4d92c)

2.1.0-9-1.3

• 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

2.1.0-9-1.2

• 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

2.1.0-9-1.1

• update payload gen module to include session_id

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

2.1.0-9-1.0

ICGC-ARGO Sanger variant calling pipeine for Whole Genome Sequencing data. It calls SNV, small Indels, CNV and SV. The pipeline also produces supplement and QC metrics as tarballs.

• Somatic SNVs called by CaVEMan
• Somatic Indels called by Pindel
• Somatic CNV called by ASCAT
• Somatic SV called by BRASS

Note: compatible argo-metadata-schema versions: 0.3.0