From 371f3376d27efcacb679e0b2b645ba6ee33be24c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Felix=20M=C3=B6lder?= Date: Wed, 23 Aug 2023 11:16:48 +0200 Subject: [PATCH] perf: update snakemake wrapper utils (#1762) ### Description ### 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). --- bio/gatk/applyvqsr/environment.yaml | 2 +- bio/gatk/variantrecalibrator/environment.yaml | 2 +- bio/picard/sortsam/environment.yaml | 2 +- bio/snpsift/genesets/environment.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bio/gatk/applyvqsr/environment.yaml b/bio/gatk/applyvqsr/environment.yaml index 76a4f8021e..405dc0c445 100644 --- a/bio/gatk/applyvqsr/environment.yaml +++ b/bio/gatk/applyvqsr/environment.yaml @@ -4,4 +4,4 @@ channels: - nodefaults dependencies: - gatk4 =4.4.0.0 - - snakemake-wrapper-utils =0.6.1 + - snakemake-wrapper-utils =0.6.2 diff --git a/bio/gatk/variantrecalibrator/environment.yaml b/bio/gatk/variantrecalibrator/environment.yaml index 8ac01153db..d566d8da5e 100644 --- a/bio/gatk/variantrecalibrator/environment.yaml +++ b/bio/gatk/variantrecalibrator/environment.yaml @@ -4,6 +4,6 @@ channels: - nodefaults dependencies: - gatk4 =4.4.0.0 - - snakemake-wrapper-utils =0.6.1 + - snakemake-wrapper-utils =0.6.2 - google-cloud-sdk - google-crc32c diff --git a/bio/picard/sortsam/environment.yaml b/bio/picard/sortsam/environment.yaml index 946a77eb9b..80adc1fa36 100644 --- a/bio/picard/sortsam/environment.yaml +++ b/bio/picard/sortsam/environment.yaml @@ -4,4 +4,4 @@ channels: - nodefaults dependencies: - picard =3.0.0 - - snakemake-wrapper-utils =0.6.1 + - snakemake-wrapper-utils =0.6.2 diff --git a/bio/snpsift/genesets/environment.yaml b/bio/snpsift/genesets/environment.yaml index 1d81cad240..5ce23548de 100644 --- a/bio/snpsift/genesets/environment.yaml +++ b/bio/snpsift/genesets/environment.yaml @@ -5,4 +5,4 @@ channels: dependencies: - snpsift =5.1 - bcftools =1.17 - - snakemake-wrapper-utils =0.6.1 + - snakemake-wrapper-utils =0.6.2