CHANGELOG

3.0.0

13 June 2024

• workflow ported to DSL2
• includes pipeline test
• includes modules tests

2.0.8

24 Apr 2024

Hotfix

• paramaterise project_code
• update submission script to use nextflow/22.10.5 module, write LSF log, and nextflow stdout and stderr to logs/<PID>_smlv* to more easily find related output

2.0.7

16 Apr 2024

Bug Fix

• revert use of scratch for working directory (/re_scratch/$USER)

2.0.6

15 Apr 2024

• increment default data version to main-programme_v18_2023-12-21
• increment module nextflow/22.10.5
• collapse logs in HPC submission
• include pipeline_info/ timeline, report, trace, and dag
• use scratch as working directory for temp files
• use the users default singularity cache

Bug Fix

• correctly count genes in input file without blank line at end of file

2.0.5

6 Oct 2023

• publish +fill-tags and missing2ref processed merged files

2.0.4

24 Aug 2023

• use standalone Nextflow binary

2.0.3

13 Jul 2023 (date of last commit)

• update s3 locations for data resources

2.0.3

13 Jul 2023 (date of last commit)

• update s3 locations for data resources

2.0.1dev

30 Jun 2023 (date of last commit)

• added parameter argument validation
• updated documentation dag

2.0

26 April 2023 (date of last commit)

• workflow re-written from WDL/Cromwell to Nextflow DSL1
• renamed to Small Variant workflow
• added configuration for both RE (Helix/HPC) and CloudRE (CloudOS)
• implemented dynamic memory/cpus for merge and annotation steps
• updated bcftools to 1.17

1.7

11 Mar 2022 (date of last commit)

• Containerised all process programs
• Updated VEP version from 99 to 105
• Added CI/CD structure