From e198ad4318fe20a9afb19ebc7b9c1ab24cc056d0 Mon Sep 17 00:00:00 2001 From: Julian Mohr <81371922+JulianMohr@users.noreply.github.com> Date: Mon, 15 Jan 2024 11:54:45 +0100 Subject: [PATCH] Update CHANGELOG.md with latest changes --- CHANGELOG.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 40b0670..e6dc99a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,14 +11,17 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), - [Fork of nf-core/test-datasets repository](https://github.com/TRON-Bioinformatics/nf-core-test-datasets) as a submodule (`tests/nf-core-test-datasets`) to introduce new test dataset provided by nf-core - New `--tools` flag with which the tool(s) to be run during pipeline execution can be specified - This `CHANGELOG.md` file and documention on old releases as well as recent development -- `CITATIONS.md` file with citations of all relevant software tools so far +- `CITATIONS.md` file with citations of all relevant software tools so far +- Support for usage of Singularity containers in `nextflow.config` (not stable and not documented yet) ### Changed -- Copy git repository from [GitHub](https://github.com/TRON-Bioinformatics/tronflow-copy-number-calling) to [GitLab](https://gitlab.rlp.net/tron/tronflow-copy-number-calling) and continue development there -- Refactor tests for GitLab CI environment +- Refactor automated tests - Extract `MERGE_REPLICATES` process from `main.nf` and store it in an individual local module at `local_modules/merge_replicates.nf` - Restructure `nextflow.config` based on nf-core's best practices (see [nf-core/sarek](https://github.com/nf-core/sarek)) +- Establish basic config and test config as standalone config files in `conf/` directory and separate these config parameters from `nextflow.config` +- Refactor local modules in `local_modules/` directory based on [nf-core/modules](https://github.com/nf-core/modules) implementation +- Replace `MERGE_REPLICATES` process by [nf-core module SAMTOOLS_MERGE](https://github.com/nf-core/modules/tree/master/modules/nf-core/samtools/merge) and integrate this module into pipeline - Update time span in `LICENSE` file ### Fixed