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feat: Goleft indexcov #2734
feat: Goleft indexcov #2734
Commits on Sep 21, 2020
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[fix] (template): Missing code in wrappers' doc. Error snakemake#187
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perf: autobump bio/bcftools/index/environment.yaml (snakemake#570)
* perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml.
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chore: release 1.15.1 (snakemake#569)
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perf: update bio/bgzip/environment.yaml. (snakemake#577)
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perf: update bio/bellerophon/environment.yaml. (snakemake#576)
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perf: update bio/assembly-stats/environment.yaml. (snakemake#575)
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perf: update bio/adapterremoval/environment.yaml. (snakemake#573)
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chore: autobump conda envs (snakemake#571)
* Add autobump action * fix paths * dbg * dbg branch * add checkout * dbg * trigger rerun * entity regex and add label * dbg * Update autobump.yml * Update autobump.yml
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perf: update bio/delly/environment.yaml. (snakemake#584)
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perf: update bio/busco/environment.yaml. (snakemake#581)
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perf: update bio/clustalo/environment.yaml. (snakemake#582)
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perf: update bio/fastp/environment.yaml. (snakemake#585)
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perf: update bio/fastq_screen/environment.yaml. (snakemake#586)
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perf: update bio/fasttree/environment.yaml. (snakemake#588)
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perf: update bio/fastqc/environment.yaml. (snakemake#587)
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perf: update bio/filtlong/environment.yaml. (snakemake#589)
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perf: update bio/freebayes/environment.yaml. (snakemake#590)
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perf: update bio/genefuse/environment.yaml. (snakemake#591)
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perf: update bio/genomepy/environment.yaml. (snakemake#592)
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chore: release 1.15.2 (snakemake#578)
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perf: autobump bio/deepvariant (snakemake#583)
Automatic update of bio/deepvariant. Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Johannes Köster <[email protected]>
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feat: bazam wrapper (snakemake#580)
<!-- 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 --> ### Description <!-- Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [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).
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chore: release 1.16.0 (snakemake#596)
🤖 I have created a release \*beep\* \*boop\* --- ## [1.16.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.15.2...v1.16.0) (2022-10-13) ### Features * bazam wrapper ([snakemake#580](https://www.github.com/snakemake/snakemake-wrappers/issues/580)) ([17e58e6](https://www.github.com/snakemake/snakemake-wrappers/commit/17e58e6f254ce429b3b76b841df29b573949e278)) ### Bug Fixes * set RG tag ([snakemake#593](https://www.github.com/snakemake/snakemake-wrappers/issues/593)) ([506a083](https://www.github.com/snakemake/snakemake-wrappers/commit/506a08391b56d4b53edda2c6555b9b9d404d4f94)) ### Performance Improvements * autobump bio/deepvariant ([snakemake#583](https://www.github.com/snakemake/snakemake-wrappers/issues/583)) ([9b7c4fe](https://www.github.com/snakemake/snakemake-wrappers/commit/9b7c4feec69d05fc7d6286dcdfdc65802cb93317)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Merge branch 'master' of https://github.com/tdayris/snakemake-wrappers
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Update bio/goleft/indexcov/wrapper.py
Co-authored-by: Filipe G. Vieira <[email protected]>
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Update bio/goleft/indexcov/wrapper.py
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