From a718777f285f175c5f6c67170b6d6440d504184b Mon Sep 17 00:00:00 2001 From: Austin Hovland <44502805+Austin-s-h@users.noreply.github.com> Date: Sat, 25 Mar 2023 15:06:16 -0400 Subject: [PATCH] perf: bump Salmon to v1.10.1 (#1168) ### Description Simple modification of salmon quant environment to install the latest version (v1.10.1) ### QC * [X] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). ``` pytest test.py -v -k test_salmon_quant ========================================================== test session starts =========================================================== platform linux -- Python 3.10.8, pytest-7.2.1, pluggy-1.0.0 -- /home/austin/mambaforge/bin/python3.10 cachedir: .pytest_cache rootdir: /home/austin/snakemake-wrappers plugins: xdist-3.1.0 collected 441 items / 440 deselected / 1 selected test.py::test_salmon_quant XPASS [100%] ============================================= 440 deselected, 1 xpassed in 71.30s (0:01:11) ============================================== ``` --- bio/salmon/quant/environment.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bio/salmon/quant/environment.yaml b/bio/salmon/quant/environment.yaml index c722a3c213..7c559ef390 100644 --- a/bio/salmon/quant/environment.yaml +++ b/bio/salmon/quant/environment.yaml @@ -1,8 +1,9 @@ channels: - - conda-forge - bioconda + - conda-forge - nodefaults dependencies: - - salmon =1.9.0 + - salmon =1.10.1 - gzip =1.12 - bzip2 =1.0.8 + \ No newline at end of file