en en pt en kn en en en en en en en en en fr en en en en en en en en en en en en en en en lt en en en en en en en en en en bn en en en en en da en en en en en en en en en en en en en en en id en pt es ja fr uk en fr es sv en en uk uk ja ja en en en en en en en en en en en en zh zh en en en en en en en en en en en en en en vi zh nb en eu th en en en en en eu eu eu eu eu th en en ja en eu eu en ja en en en en en en en zh en ja de ja th en es en en th eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu eu ja fi zh zh eu eu es ja eu uk th th th th en ja zh eu eu th th en ja en en en en en
We invite anybody to contribute to the Snakemake Wrapper Repository. If you want to contribute we suggest the following procedure:
Locally, create a new branch: git checkout -b my-new-snakemake-wrapper
Commit your contributions to that branch and push them to your fork: git push -u origin my-new-snakemake-wrapper
The pull request will be reviewed and included as fast as possible. If your pull request does not get a review quickly, you can @mention   previous contributors to a particular wrapper (git blame) or regular contributors that you think might be able to give a review. Contributions should follow the coding style of the already present examples, i.e.:
provide a meta.yaml that describes the wrapper (see the meta.yaml documentation below)
provide an environment.yaml which lists all required software packages and follows the respective best practices. The packages should be available for installation via the default anaconda channels or via the conda channels bioconda or conda-forge. Other sustainable community maintained channels are possible as well.
add a wrapper.py or wrapper.R file that can deal with arbitrary input: and output: paths.
provide a minimal test case in a subfolder called test, with an example Snakefile that shows how to use the wrapper (rule names should be descriptive and written in snake_case), some minimal testing data (also check existing wrappers for suitable data) and add an invocation of the test in test.py
ensure consistent formatting of Python files and linting of Snakefiles.
The following fields are available to use in the wrapper meta.yaml file. All, except those marked optional, should be provided.
name: The name of the wrapper.
description: a description of what the wrapper does.
url: URL to the wrapper tool webpage.
authors: A sequence of names of the people who have contributed to the wrapper.
input: A mapping or sequence of required inputs for the wrapper.
output: A mapping or sequence of output(s) from the wrapper.
params (optional): A mapping of parameters that can be used in the wrapper’s params directive. If no parameters are used for the wrapper, this field can be omitted.
notes (optional): Anything of note that does not fit into the scope of the other fields.
You can add a newline to the rendered text in these fields with the addition of |nl|
name: seqtk mergepe description: Interleave two paired-end FASTA/Q files url: https://github.com/lh3/seqtk authors: - Michael Hall input: - paired fastq files - can be compressed. output: - > a single, interleaved FASTA/Q file. By default, the output will be compressed, use the param ``compress_lvl`` to change this. params: compress_lvl: > Regulate the speed of compression using the specified digit, where 1 indicates the fastest compression method (less compression) and 9 indicates the slowest compression method (best compression). 0 is no compression. 11 gives a few percent better compression at a severe cost in execution time, using the zopfli algorithm. The default is 6. notes: Multiple threads can be used during compression of the output file with ``pigz``.
Please ensure Python files such as test.py and wrapper.py are formatted with black. Additionally, please format your test Snakefile with snakefmt.
Please lint your test Snakefile with:
If you want to debug your contribution locally (before creating a pull request), you can install all dependencies with mamba (or conda). Install miniconda with the channels as described for bioconda and set up an environment with the necessary dependencies and activate it:
mamba create -n test-snakemake-wrappers snakemake pytest conda snakefmt black conda activate test-snakemake-wrappers
Afterwards, from the main directory of the repo, you can run the test(s) for your contribution by specifying an expression that matches the name(s) of your test(s) via the -k option of pytest:
pytest test.py -v -k your_test
If you also want to test the docs generation locally, create another environment and activate it:
mamba create -n test-snakemake-wrapper-docs sphinx sphinx_rtd_theme pyyaml sphinx-copybutton conda activate test-snakemake-wrapper-docs
Then, enter the respective directory and build the docs:
cd docs make html
If it runs through, you can open the main page at docs/_build/html/index.html in a web browser. If you want to start fresh, you can clean up the build with make clean.