From 3e72a7e2560da1f86682aa82a1a248b221cb57e7 Mon Sep 17 00:00:00 2001 From: Will Bradshaw Date: Wed, 27 Nov 2024 15:27:10 +0000 Subject: [PATCH] Cleaned up changelog and versioning for merge to master --- CHANGELOG.md | 33 +++++++++++++++++++-------------- pipeline-version.txt | 2 +- 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 48c668a..c049cb2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,23 +1,28 @@ -# v2.5.2 (in progress) -- 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 -- Added nf-test configurable end-to-end testing: - - Implemented test suite in `tests/main.nf.test` - - Added Github Actions workflow in `.github/workflows/end-to-end.yml` -- Updated test dataset with new sample data in `test-data/samplesheet.csv`. The old test dataset, `test` has been removed, for this new dataset. -- 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). +# v2.5.2 +- 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 -- Removed redundant subsetting statement from TAXONOMY workflow. -- Added --group_across_illumina_lanes option to generate_samplesheet -- 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 +- 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 # v2.5.1 - Enabled extraction of BBDuk-subset putatively-host-viral raw reads for downstream chimera detection. diff --git a/pipeline-version.txt b/pipeline-version.txt index 73462a5..f225a78 100644 --- a/pipeline-version.txt +++ b/pipeline-version.txt @@ -1 +1 @@ -2.5.1 +2.5.2