Rna Seq Star Deseq2 Versions Save

2.1.1 (2024-03-25)

Bug Fixes

• release-please branch to master and set permissions (#79) (4b781cf)
• update to using storage plugin ftp (#76) (0f18be7)

Performance Improvements

• update all wrapper to latest v3.5.3 (#78) (bc9ab71)

Just a quick release with some fixes that have accumulated, so that deployment via snakedeploy and the snakemake workflow catalog will also include those:

• fix: Fixing workflow for single-end sequencing #70
• fix: update gffults & qc #69

This is a major improvement of this workflow, bringing it up to date and extending its functionality. Many thanks to all of the people who reported problems and suggested improvements over the last 1.5 years. I'll try to name all here, but please ping me if I forgot anyone. There was input and contributions from (in no particular order): @isaacvock, @kilpert, @dlaehnemann, @jonathandmoore, @cbp44, @aryazand, @iwv2, @FelixMoelder, @johanneskoester, @svenrahmann

Major change in workflow configuration (/ configurability):

• feat!: generalize away condition (PR #66): The workflow can now fully use DESeq2's flexibility in its model setup and does not make use of a particular name for the variable_of_interest any more. Instead, there is a new, fully explained, and reasonably intuitive configuration setup in the config.yaml for this, including linkouts to the relevant docs and an explanation in the snakemake workflow catalog docs (that have been improved for unchanged features, as well). Also, this setup and the workflow in general is now more comprehensively tested.

Also lots of smaller fixes:

• fix: stable column ordering in count-matrix.py (PR #60)
• updated all wrappers to a current version (PR #59) (also updates GitHub Actions submodule checkout)
• fixed inconsistent file naming to all underscores ({sample}_{unit} vs. {sample)-{unit} that we had in some places, PR #61)
• fix: make get_deseq2_threads() proper function call in diffexp.smk (PR #62)
• fix: make specification of SRA samples in samples.tsv work, fixes in common.smk (PR #63)
• fix: cutadapt wrapper params from others: to extra: (originally suggested by @kilpert: https://github.com/snakemake-workflows/rna-seq-star-deseq2/commit/f816550598c29ed2840e21b31a592ce87a7ebcfa)
• feat: add basic wildcard_constraints for safer sample and unit names (originally suggested by @kilpert: https://github.com/snakemake-workflows/rna-seq-star-deseq2/commit/5431e08f31890869d606e720993b17bbd44391de)
• fix: fix rule align (star) parameters and make gtf an actual input (https://github.com/snakemake-workflows/rna-seq-star-deseq2/commit/fdce8475853745fa41429af5fe7da0726efdbc50)
• some smaller cleanup of outdated comments
• addressing of some R lints

And a new feature addition (hasn't kicked in yet, this will probably come with the next PR merge):

• feat: add release-please and use conventional commits for it (PR #64)

• deseq_init rule now outputs normalized counts as well (@jafors).
• Updated software versions (@lparsons, @jafors).
• Convert gene IDs to symbols (@jafors).

Format workflow according to Python and Snakemake style guides (black and snakefmt).

Fixed naming of snakemake-workflow-catalog configuration file.

• add protocol strandedness awareness (@matrs)
• make trimming optional (@sschmeier)
• adapt to latest best practices and structure (@jafors)

Added QC.