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<!-- Ensure that the PR title follows conventional commit style (<type>: <description>)--> <!-- Possible types are here: https://github.com/commitizen/conventional-commit-types/blob/master/index.json --> <!-- Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] 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 * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced a comprehensive Conda environment configuration for the `rseqc` package to facilitate reproducible bioinformatics workflows. - Added a new tool for summarizing mapping statistics from BAM/SAM files, complete with metadata and functionality descriptions. - Implemented a Snakemake rule for processing BAM files, enhancing the integration of BAM analysis into workflows. - Created a wrapper script for executing the BAM statistics tool within Snakemake. - **Tests** - Added a new test function to improve testing coverage for the `bio/rseqc` functionality related to BAM statistics. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: tdayris <tdayris@gustaveroussy.fr> Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Felix Mölder <felix.moelder@uni-due.de> Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>
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| # This file may be used to create an environment using: | ||
| # $ conda create --name <env> --file <this file> | ||
| # platform: linux-64 | ||
| @EXPLICIT | ||
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| https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef | ||
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| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - nodefaults | ||
| dependencies: | ||
| - rseqc=5.0.3 |
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| name: RSeQC bam_stat.py | ||
| url: https://rseqc.sourceforge.net/#bam-stat-py | ||
| description: > | ||
| Summarizing mapping statistics of a BAM or SAM file. | ||
| authors: | ||
| - Thibault Dayris | ||
| input: | ||
| - Path to BAM/SAM file(s) to summarize. | ||
| output: | ||
| - Path to summary | ||
| params: | ||
| - extra: Optional argument basides `--input-file` | ||
| notes: > | ||
| Only mapping quality can be provided as optional parameters, since `--help` and `--version` do not produce summary. |
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| rule test_rseqc_bam_stat: | ||
| input: | ||
| "a.bam", | ||
| output: | ||
| "a.stats", | ||
| threads: 1 | ||
| params: | ||
| extra="--mapq 5", | ||
| log: | ||
| "bastat.log", | ||
| wrapper: | ||
| "master/bio/rseqc/bam_stat" |
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| # coding: utf-8 | ||
|
|
||
| __author__ = "Thibault Dayris" | ||
| __mail__ = "thibault.dayris@gustaveroussy.fr" | ||
| __copyright__ = "Copyright 2024, Thibault Dayris" | ||
| __license__ = "MIT" | ||
|
|
||
| from snakemake import shell | ||
|
|
||
| extra = snakemake.params.get("extra", "") | ||
| log = snakemake.log_fmt_shell(stdout=False, stderr=True) | ||
|
|
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| shell("bam_stat.py --input-file {snakemake.input[0]} > {snakemake.output} {log}") |
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