Skip to content

CHANGELOG

v3.1.2

latest

  • use merge flag --force-single to allow edge case merge of single file, added in bftools release 1.20

Use the latest workflow version

Please always use the latest available workflow version, unless explicitly instructed otherwise. All earlier versions are no longer supported. The change history is provided below for reference.

v3.1.1

  • renamed configuration profiles: cluster -> hpc, cloud -> cloudos
  • included latest version check and warning
  • included message to create scratch dir and update submission script
  • added workflow manifest

v3.1.0

18 Oct 2024

  • updated Nextflow version
    • Nextflow 24.04.2
    • nf-schema@2.0.0
  • updated process containers
    • bcftools 1.20
    • linux 24.04
    • python 3.12.3
  • added parameter validation, help, and summary logs
  • added samplesheet validation
  • updated optional input samplesheet structure. Samplesheet is now a comma-separated values (CSV) file with header (see Input files)
  • supported data sources (germline only): 100KGP
  • current data release (from which samples are drawn when no samplesheet is supplied): main-programme/main-programme_v18_2023-12-21
  • configuration profile names changed: cluster -> hpc, cloud -> cloudos

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