v2.5.2

[willbradshaw]

From CHANGELOG:

• Changes to default read filtering:
  • Relaxed FASTP quality filtering (--cut_mean_quality and --average_qual reduced from 25 to 20).
  • Relaxed BBDUK viral filtering (switched from 3 21-mers to 1 24-mer).
• Overhauled BLAST validation functionality:
  • BLAST now runs on forward and reverse reads independently
  • BLAST output filtering no longer assumes specific filename suffixes
  • Paired BLAST output includes more information
  • RUN_VALIDATION can now directly take in FASTA files instead of a virus read DB
  • Fixed issues with publishing BLAST output under new Nextflow version
• Implemented nf-test for end-to-end testing of pipeline functionality
  • Implemented test suite in tests/main.nf.test
  • Reconfigured INDEX workflow to enable generation of miniature index directories for testing
  • Added Github Actions workflow in .github/workflows/end-to-end.yml
  • Pull requests will now fail if any of INDEX, RUN, or RUN_VALIDATION crashes when run on test data.
  • Generated first version of new, curated test dataset for testing RUN workflow. Samplesheet and config file are available in test-data. The previous test dataset in test has been removed.
• Implemented S3 auto-cleanup:
  • Added tags to published files to facilitate S3 auto-cleanup
  • Added S3 lifecycle configuration file to ref, along with a script in bin to add it to an S3 bucket
• Minor changes
  • Added logic to check if grouping variable in nextflow.config matches the input samplesheet, if it doesn't, the code throws an error.
  • Externalized resource specifications to resources.config, removing hardcoded CPU/memory values
  • Renamed index-params.json to params-index.json to avoid clash with Github Actions
  • Removed redundant subsetting statement from TAXONOMY workflow.
  • Added --group_across_illumina_lanes option to generate_samplesheet