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feat: Bowtie2 meta #1586
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feat: Bowtie2 meta #1586
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* 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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* 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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Automatic update of bio/deepvariant. Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
<!-- 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).
🤖 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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🤖 I have created a release \*beep\* \*boop\* --- ## [2.3.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.2.1...v2.3.0) (2023-08-04) ### Features * Bowtie2 meta ([#1586](https://www.github.com/snakemake/snakemake-wrappers/issues/1586)) ([d8edd7b](https://www.github.com/snakemake/snakemake-wrappers/commit/d8edd7bb2d282f097685d593abe1d2f83b3f1120)) * enable output of unmapped reads ([#1549](https://www.github.com/snakemake/snakemake-wrappers/issues/1549)) ([bff21bc](https://www.github.com/snakemake/snakemake-wrappers/commit/bff21bc8f644806a4f49ab68e1d8b70464460e02)) * Gatk calculate contamination ([#1547](https://www.github.com/snakemake/snakemake-wrappers/issues/1547)) ([4f73135](https://www.github.com/snakemake/snakemake-wrappers/commit/4f73135020da21e5e472acc42f7b229998788010)) ### Bug Fixes * freebayes wrapper ([#1715](https://www.github.com/snakemake/snakemake-wrappers/issues/1715)) ([8656035](https://www.github.com/snakemake/snakemake-wrappers/commit/865603539bba2e516acf50a7c38186810f1da051)) ### Performance Improvements * autobump bio/bazam ([#1555](https://www.github.com/snakemake/snakemake-wrappers/issues/1555)) ([9c5d121](https://www.github.com/snakemake/snakemake-wrappers/commit/9c5d121c561e00b3963e87d6f84020043fdaea2c)) * autobump bio/bcftools/call ([#1691](https://www.github.com/snakemake/snakemake-wrappers/issues/1691)) ([c6b88eb](https://www.github.com/snakemake/snakemake-wrappers/commit/c6b88ebc62f3153f636431acca6526a2ffe972da)) * autobump bio/bcftools/call ([#1710](https://www.github.com/snakemake/snakemake-wrappers/issues/1710)) ([7430a6f](https://www.github.com/snakemake/snakemake-wrappers/commit/7430a6f765e06d7684a265d89f44145bad1e7157)) * autobump bio/bcftools/concat ([#1531](https://www.github.com/snakemake/snakemake-wrappers/issues/1531)) ([d6edd85](https://www.github.com/snakemake/snakemake-wrappers/commit/d6edd85e222310bbdd28369f92186c7e33695d63)) * autobump bio/bcftools/concat ([#1603](https://www.github.com/snakemake/snakemake-wrappers/issues/1603)) ([5b72872](https://www.github.com/snakemake/snakemake-wrappers/commit/5b72872754d8eb177f064db70dc634bd640e6944)) * autobump bio/bcftools/concat ([#1630](https://www.github.com/snakemake/snakemake-wrappers/issues/1630)) ([cd70d77](https://www.github.com/snakemake/snakemake-wrappers/commit/cd70d7729504dcf7afea4557191e335f3efeeceb)) * autobump bio/bcftools/concat ([#1661](https://www.github.com/snakemake/snakemake-wrappers/issues/1661)) ([4455dcc](https://www.github.com/snakemake/snakemake-wrappers/commit/4455dcc8af9195e4b44ffdeb053c12b93a3ea858)) * autobump bio/bcftools/concat ([#1692](https://www.github.com/snakemake/snakemake-wrappers/issues/1692)) ([a7ece62](https://www.github.com/snakemake/snakemake-wrappers/commit/a7ece6239b043bf8583ac568427442d3021b68b4)) * autobump bio/bcftools/filter ([#1609](https://www.github.com/snakemake/snakemake-wrappers/issues/1609)) ([30d5d64](https://www.github.com/snakemake/snakemake-wrappers/commit/30d5d64904b956e2769b6e804e0972cfc0b4a60b)) * autobump bio/bcftools/filter ([#1637](https://www.github.com/snakemake/snakemake-wrappers/issues/1637)) ([772a77b](https://www.github.com/snakemake/snakemake-wrappers/commit/772a77baa7073666d2ddc09a377768acb3ca8d59)) * autobump bio/bcftools/filter ([#1676](https://www.github.com/snakemake/snakemake-wrappers/issues/1676)) ([1e69c25](https://www.github.com/snakemake/snakemake-wrappers/commit/1e69c25c5e7f27083bdd3c31569c3c5e57739071)) * autobump bio/bcftools/filter ([#1703](https://www.github.com/snakemake/snakemake-wrappers/issues/1703)) ([c5224a5](https://www.github.com/snakemake/snakemake-wrappers/commit/c5224a5b7adc3245dd48783550a9da505a2cf577)) * autobump bio/bcftools/index ([#1537](https://www.github.com/snakemake/snakemake-wrappers/issues/1537)) ([d403067](https://www.github.com/snakemake/snakemake-wrappers/commit/d4030670e039333b146989bff0437155e6e00944)) * autobump bio/bcftools/index ([#1602](https://www.github.com/snakemake/snakemake-wrappers/issues/1602)) ([45e0d82](https://www.github.com/snakemake/snakemake-wrappers/commit/45e0d827bdc05bcb2b508fa1be3252b747badfb1)) * autobump bio/bcftools/merge ([#1558](https://www.github.com/snakemake/snakemake-wrappers/issues/1558)) ([18ec70f](https://www.github.com/snakemake/snakemake-wrappers/commit/18ec70f9a8c7d47cdfd0b85aa52ba03879ffa5b9)) * autobump bio/bcftools/mpileup ([#1620](https://www.github.com/snakemake/snakemake-wrappers/issues/1620)) ([6bc5006](https://www.github.com/snakemake/snakemake-wrappers/commit/6bc50063bcb60d6cf0d84221c72d4cc5fae174f0)) * autobump bio/bcftools/mpileup ([#1683](https://www.github.com/snakemake/snakemake-wrappers/issues/1683)) ([dc033c5](https://www.github.com/snakemake/snakemake-wrappers/commit/dc033c50f08819c8a63090f5663fa1c829dced79)) * autobump bio/bcftools/norm ([#1680](https://www.github.com/snakemake/snakemake-wrappers/issues/1680)) ([0f32280](https://www.github.com/snakemake/snakemake-wrappers/commit/0f32280c4f6725564dee2bb784badca4bae39823)) * autobump bio/bcftools/norm ([#1706](https://www.github.com/snakemake/snakemake-wrappers/issues/1706)) ([6822f7a](https://www.github.com/snakemake/snakemake-wrappers/commit/6822f7a8e28edda64b3771c1f4d46687f64b8691)) * autobump bio/bcftools/reheader ([#1595](https://www.github.com/snakemake/snakemake-wrappers/issues/1595)) ([83455a3](https://www.github.com/snakemake/snakemake-wrappers/commit/83455a397f24bedbe811939cf012f1088fa758cd)) * autobump bio/bcftools/reheader ([#1638](https://www.github.com/snakemake/snakemake-wrappers/issues/1638)) ([6c63212](https://www.github.com/snakemake/snakemake-wrappers/commit/6c63212e503cbdfa43250616ee0359116709f017)) * autobump bio/bcftools/sort ([#1575](https://www.github.com/snakemake/snakemake-wrappers/issues/1575)) ([92b11ed](https://www.github.com/snakemake/snakemake-wrappers/commit/92b11ed004513e7118c0d2e0bd0f58cc65b251f7)) * autobump bio/bcftools/view ([#1618](https://www.github.com/snakemake/snakemake-wrappers/issues/1618)) ([e7c3390](https://www.github.com/snakemake/snakemake-wrappers/commit/e7c3390069dfcdf4da61199aa9d2d26569d94720)) * autobump bio/bcftools/view ([#1631](https://www.github.com/snakemake/snakemake-wrappers/issues/1631)) ([0756847](https://www.github.com/snakemake/snakemake-wrappers/commit/0756847ed1e837192d5310fbbca89305d4617295)) * autobump bio/bellerophon ([#1614](https://www.github.com/snakemake/snakemake-wrappers/issues/1614)) ([d9c9b0b](https://www.github.com/snakemake/snakemake-wrappers/commit/d9c9b0bda61505b66413b10590787d72ec39eab4)) * autobump bio/bellerophon ([#1646](https://www.github.com/snakemake/snakemake-wrappers/issues/1646)) ([5c47391](https://www.github.com/snakemake/snakemake-wrappers/commit/5c473918eb84a7b3bc6d4fbbb7d4587b12b0c38f)) * autobump bio/bgzip ([#1652](https://www.github.com/snakemake/snakemake-wrappers/issues/1652)) ([3cc38ac](https://www.github.com/snakemake/snakemake-wrappers/commit/3cc38acaa6374a4425d8cac3fc5b72c6c3126747)) * autobump bio/bismark/bismark2report ([#1714](https://www.github.com/snakemake/snakemake-wrappers/issues/1714)) ([6d95e56](https://www.github.com/snakemake/snakemake-wrappers/commit/6d95e56da2e2ed09133cb20ea2608f94d1483228)) * autobump bio/bismark/bismark2summary ([#1594](https://www.github.com/snakemake/snakemake-wrappers/issues/1594)) ([c7a0448](https://www.github.com/snakemake/snakemake-wrappers/commit/c7a044874f51c6231c8551b1e5b36d7302732385)) * autobump bio/bismark/bismark2summary ([#1679](https://www.github.com/snakemake/snakemake-wrappers/issues/1679)) ([135dabc](https://www.github.com/snakemake/snakemake-wrappers/commit/135dabc0f7b5f349cf43468be5899054e8f1d478)) * autobump bio/bismark/bismark2summary ([#1687](https://www.github.com/snakemake/snakemake-wrappers/issues/1687)) ([3cf315a](https://www.github.com/snakemake/snakemake-wrappers/commit/3cf315a96c213e92ef8ba6712b259d60840913d0)) * autobump bio/bowtie2/align ([#1634](https://www.github.com/snakemake/snakemake-wrappers/issues/1634)) ([477d1ab](https://www.github.com/snakemake/snakemake-wrappers/commit/477d1ab674e32642b0d46885964889230371193e)) * autobump bio/bustools/sort ([#1688](https://www.github.com/snakemake/snakemake-wrappers/issues/1688)) ([7d37969](https://www.github.com/snakemake/snakemake-wrappers/commit/7d3796958009213f62637e073b801974d82aab52)) * autobump bio/bustools/text ([#1523](https://www.github.com/snakemake/snakemake-wrappers/issues/1523)) ([08f0e0a](https://www.github.com/snakemake/snakemake-wrappers/commit/08f0e0a0b4033fff6aa1d30b0e0d315ae5f3086a)) * autobump bio/bwa-mem2/mem ([#1669](https://www.github.com/snakemake/snakemake-wrappers/issues/1669)) ([92ba532](https://www.github.com/snakemake/snakemake-wrappers/commit/92ba53269f589f156b8827d6188956fdad70c678)) * autobump bio/bwa/mem ([#1656](https://www.github.com/snakemake/snakemake-wrappers/issues/1656)) ([03224f2](https://www.github.com/snakemake/snakemake-wrappers/commit/03224f2c01a67f0df2efef4162b6f0b9c8b7aa41)) * autobump bio/dada2/add-species ([#1522](https://www.github.com/snakemake/snakemake-wrappers/issues/1522)) ([2f2ccc6](https://www.github.com/snakemake/snakemake-wrappers/commit/2f2ccc6b67dd1edd17eca576791f8be38bbaa675)) * autobump bio/dada2/assign-species ([#1563](https://www.github.com/snakemake/snakemake-wrappers/issues/1563)) ([adf781e](https://www.github.com/snakemake/snakemake-wrappers/commit/adf781e04c33988518b194aa322ac861ee0ebe06)) * autobump bio/dada2/assign-taxonomy ([#1551](https://www.github.com/snakemake/snakemake-wrappers/issues/1551)) ([31c3b9a](https://www.github.com/snakemake/snakemake-wrappers/commit/31c3b9a9e146de3a4337108f15702e8c175f457b)) * autobump bio/dada2/collapse-nomismatch ([#1554](https://www.github.com/snakemake/snakemake-wrappers/issues/1554)) ([db5b2ea](https://www.github.com/snakemake/snakemake-wrappers/commit/db5b2ea65ea7e811b54eb7e574a72d8cd257aa61)) * autobump bio/dada2/dereplicate-fastq ([#1671](https://www.github.com/snakemake/snakemake-wrappers/issues/1671)) ([2386b66](https://www.github.com/snakemake/snakemake-wrappers/commit/2386b66863189046d1df76bb5d16d9c8f9263110)) * autobump bio/dada2/filter-trim ([#1641](https://www.github.com/snakemake/snakemake-wrappers/issues/1641)) ([c58bcfb](https://www.github.com/snakemake/snakemake-wrappers/commit/c58bcfb860af2598f83d06d81156ea52eb15988c)) * autobump bio/dada2/learn-errors ([#1574](https://www.github.com/snakemake/snakemake-wrappers/issues/1574)) ([da832b1](https://www.github.com/snakemake/snakemake-wrappers/commit/da832b10177fd96b57b7475ee16c1fa39d86f5ba)) * autobump bio/dada2/make-table ([#1678](https://www.github.com/snakemake/snakemake-wrappers/issues/1678)) ([a235b2f](https://www.github.com/snakemake/snakemake-wrappers/commit/a235b2f33a35de1ce4e807a0cdb5d14d4afc1330)) * autobump bio/dada2/merge-pairs ([#1588](https://www.github.com/snakemake/snakemake-wrappers/issues/1588)) ([17d69a0](https://www.github.com/snakemake/snakemake-wrappers/commit/17d69a05c188d5072542db1876255f63dbb7368b)) * autobump bio/dada2/merge-pairs ([#1689](https://www.github.com/snakemake/snakemake-wrappers/issues/1689)) ([ef65a5f](https://www.github.com/snakemake/snakemake-wrappers/commit/ef65a5f39e403c2e2d8e1d61206d9854fcfa60c4)) * autobump bio/dada2/merge-pairs ([#1712](https://www.github.com/snakemake/snakemake-wrappers/issues/1712)) ([bc6d079](https://www.github.com/snakemake/snakemake-wrappers/commit/bc6d0798881a572d73876475ec989d7ddb4b532d)) * autobump bio/dada2/quality-profile ([#1534](https://www.github.com/snakemake/snakemake-wrappers/issues/1534)) ([05d12b3](https://www.github.com/snakemake/snakemake-wrappers/commit/05d12b309df632f6d45683b63843cd300333fde5)) * autobump bio/dada2/remove-chimeras ([#1541](https://www.github.com/snakemake/snakemake-wrappers/issues/1541)) ([7282994](https://www.github.com/snakemake/snakemake-wrappers/commit/7282994399a03f3f693b7efcc0935f2c2a71739c)) * autobump bio/dada2/sample-inference ([#1702](https://www.github.com/snakemake/snakemake-wrappers/issues/1702)) ([a82d8fc](https://www.github.com/snakemake/snakemake-wrappers/commit/a82d8fc9da618ae57572a2e8d5899c1ea767dde6)) * autobump bio/deeptools/alignmentsieve ([#1635](https://www.github.com/snakemake/snakemake-wrappers/issues/1635)) ([b01bb82](https://www.github.com/snakemake/snakemake-wrappers/commit/b01bb82378638f404a77959c9e2725c81480f0ec)) * autobump bio/deeptools/plotheatmap ([#1561](https://www.github.com/snakemake/snakemake-wrappers/issues/1561)) ([faf49e2](https://www.github.com/snakemake/snakemake-wrappers/commit/faf49e20a7e19592bde11835206b2427b9104c87)) * autobump bio/deseq2/deseqdataset ([#1633](https://www.github.com/snakemake/snakemake-wrappers/issues/1633)) ([176be53](https://www.github.com/snakemake/snakemake-wrappers/commit/176be53f11bde39e27bea97977eeedf72fdbd2fb)) * autobump bio/diamond/blastp ([#1570](https://www.github.com/snakemake/snakemake-wrappers/issues/1570)) ([3f61c8f](https://www.github.com/snakemake/snakemake-wrappers/commit/3f61c8fdb7c309ecc6655ff138467055313808e2)) * autobump bio/diamond/blastx ([#1670](https://www.github.com/snakemake/snakemake-wrappers/issues/1670)) ([0eaf267](https://www.github.com/snakemake/snakemake-wrappers/commit/0eaf267181dce43233e7708101593ee3805917c2)) * autobump bio/diamond/makedb ([#1711](https://www.github.com/snakemake/snakemake-wrappers/issues/1711)) ([e4bc2e4](https://www.github.com/snakemake/snakemake-wrappers/commit/e4bc2e4a2482a579e72821152d7964f8a57df99c)) * autobump bio/fastqc ([#1540](https://www.github.com/snakemake/snakemake-wrappers/issues/1540)) ([1e0d23e](https://www.github.com/snakemake/snakemake-wrappers/commit/1e0d23e8264738a256bc7059c73533befdc56e3f)) * autobump bio/fgbio/annotatebamwithumis ([#1572](https://www.github.com/snakemake/snakemake-wrappers/issues/1572)) ([47e4c62](https://www.github.com/snakemake/snakemake-wrappers/commit/47e4c6284b11f6aab4aae962a2d32df9a6c13b26)) * autobump bio/fgbio/collectduplexseqmetrics ([#1648](https://www.github.com/snakemake/snakemake-wrappers/issues/1648)) ([e8fd7f0](https://www.github.com/snakemake/snakemake-wrappers/commit/e8fd7f0cf0f21384738998af7ea3114ac3f5374f)) * autobump bio/gatk/applybqsr ([#1589](https://www.github.com/snakemake/snakemake-wrappers/issues/1589)) ([5ebf186](https://www.github.com/snakemake/snakemake-wrappers/commit/5ebf1868c5e30ed4b327e37bbff5cc4766abd49b)) * autobump bio/gatk/applybqsrspark ([#1578](https://www.github.com/snakemake/snakemake-wrappers/issues/1578)) ([007a4d1](https://www.github.com/snakemake/snakemake-wrappers/commit/007a4d11c21f5f3bb391b9d4288e549b3a7185ac)) * autobump bio/gatk/applyvqsr ([#1544](https://www.github.com/snakemake/snakemake-wrappers/issues/1544)) ([0c45d39](https://www.github.com/snakemake/snakemake-wrappers/commit/0c45d3911700546cd743c099a521cd011d0c28a2)) * autobump bio/gatk/baserecalibrator ([#1535](https://www.github.com/snakemake/snakemake-wrappers/issues/1535)) ([0d006e0](https://www.github.com/snakemake/snakemake-wrappers/commit/0d006e09645897807a24cd6af5963fc5155dc03a)) * autobump bio/gatk/baserecalibrator ([#1581](https://www.github.com/snakemake/snakemake-wrappers/issues/1581)) ([153b20b](https://www.github.com/snakemake/snakemake-wrappers/commit/153b20bcfdad658be7959f1b95b6bfb0aa03e3a9)) * autobump bio/gatk/baserecalibratorspark ([#1600](https://www.github.com/snakemake/snakemake-wrappers/issues/1600)) ([2d5a263](https://www.github.com/snakemake/snakemake-wrappers/commit/2d5a263bfec71b8d8ca07e7a558453c6f0ef11a3)) * autobump bio/gatk/baserecalibratorspark ([#1649](https://www.github.com/snakemake/snakemake-wrappers/issues/1649)) ([207026c](https://www.github.com/snakemake/snakemake-wrappers/commit/207026c9caa39af09e62f300811bf311a886e9a7)) * autobump bio/gatk/callcopyratiosegments ([#1527](https://www.github.com/snakemake/snakemake-wrappers/issues/1527)) ([5a4741a](https://www.github.com/snakemake/snakemake-wrappers/commit/5a4741acd39642095459cdbaec7b749fb8354ae8)) * autobump bio/gatk/callcopyratiosegments ([#1557](https://www.github.com/snakemake/snakemake-wrappers/issues/1557)) ([4c788df](https://www.github.com/snakemake/snakemake-wrappers/commit/4c788df8f68823bdff87d00a81df6b8541e49213)) * autobump bio/gatk/cleansam ([#1599](https://www.github.com/snakemake/snakemake-wrappers/issues/1599)) ([a58bbfe](https://www.github.com/snakemake/snakemake-wrappers/commit/a58bbfe6d15e005bad9cde29da3d780c1c90a601)) * autobump bio/gatk/cleansam ([#1659](https://www.github.com/snakemake/snakemake-wrappers/issues/1659)) ([299198f](https://www.github.com/snakemake/snakemake-wrappers/commit/299198fab4635546351653d0fbe5e5e39873f1c2)) * autobump bio/gatk/collectalleliccounts ([#1719](https://www.github.com/snakemake/snakemake-wrappers/issues/1719)) ([bf74f2f](https://www.github.com/snakemake/snakemake-wrappers/commit/bf74f2f922a2164c3cf6315c2fc2a9d4d505c3d9)) * autobump bio/gatk/collectreadcounts ([#1684](https://www.github.com/snakemake/snakemake-wrappers/issues/1684)) ([dae6459](https://www.github.com/snakemake/snakemake-wrappers/commit/dae64590862e492df1ba7e53cce41e9557688ee5)) * autobump bio/gatk/denoisereadcounts ([#1704](https://www.github.com/snakemake/snakemake-wrappers/issues/1704)) ([c398633](https://www.github.com/snakemake/snakemake-wrappers/commit/c39863369932331f70c5cc0175a0a903b41c6181)) * autobump bio/gatk/depthofcoverage ([#1601](https://www.github.com/snakemake/snakemake-wrappers/issues/1601)) ([45248d4](https://www.github.com/snakemake/snakemake-wrappers/commit/45248d45a0684f08a0697129b146f601822283b6)) * autobump bio/gatk/depthofcoverage ([#1667](https://www.github.com/snakemake/snakemake-wrappers/issues/1667)) ([7ffe876](https://www.github.com/snakemake/snakemake-wrappers/commit/7ffe876823b1b02e9c96821f60671d6b3a506d0c)) * autobump bio/gatk/filtermutectcalls ([#1668](https://www.github.com/snakemake/snakemake-wrappers/issues/1668)) ([8924792](https://www.github.com/snakemake/snakemake-wrappers/commit/89247926b6cd852161abe9765f3e66bb96c73a6d)) * autobump bio/gatk/filtermutectcalls ([#1713](https://www.github.com/snakemake/snakemake-wrappers/issues/1713)) ([30c7e9b](https://www.github.com/snakemake/snakemake-wrappers/commit/30c7e9bbcf3cea2188bca967c4a358f69cbfe8bf)) * autobump bio/gatk/genomicsdbimport ([#1722](https://www.github.com/snakemake/snakemake-wrappers/issues/1722)) ([eef7b43](https://www.github.com/snakemake/snakemake-wrappers/commit/eef7b43efdfbd0a92e7cc3ef423cd774ef0ab171)) * autobump bio/gatk/genotypegvcfs ([#1560](https://www.github.com/snakemake/snakemake-wrappers/issues/1560)) ([b64e056](https://www.github.com/snakemake/snakemake-wrappers/commit/b64e056c8eca0d12159bb73d225dc61eae3bef5d)) * autobump bio/gatk/haplotypecaller ([#1705](https://www.github.com/snakemake/snakemake-wrappers/issues/1705)) ([ec9815e](https://www.github.com/snakemake/snakemake-wrappers/commit/ec9815eaf4ecc8e0b4b85db2bd0940961b0548b6)) * autobump bio/gatk/intervallisttobed ([#1622](https://www.github.com/snakemake/snakemake-wrappers/issues/1622)) ([3d5215d](https://www.github.com/snakemake/snakemake-wrappers/commit/3d5215dd5d0da5a22c93f28374a5d36919ff97a6)) * autobump bio/gatk/intervallisttobed ([#1647](https://www.github.com/snakemake/snakemake-wrappers/issues/1647)) ([e4c13a2](https://www.github.com/snakemake/snakemake-wrappers/commit/e4c13a2cd9b9b8ecf9314e1bc6ee5b59875339c0)) * autobump bio/gatk/intervallisttobed ([#1663](https://www.github.com/snakemake/snakemake-wrappers/issues/1663)) ([9654834](https://www.github.com/snakemake/snakemake-wrappers/commit/9654834c9c5f9827e9a27687a3ce17034a2ce8b2)) * autobump bio/gatk/intervallisttobed ([#1693](https://www.github.com/snakemake/snakemake-wrappers/issues/1693)) ([8acf652](https://www.github.com/snakemake/snakemake-wrappers/commit/8acf6520e7ec204e0a4e663834632d8d1efc6a89)) * autobump bio/gatk/learnreadorientationmodel ([#1625](https://www.github.com/snakemake/snakemake-wrappers/issues/1625)) ([bd0fa42](https://www.github.com/snakemake/snakemake-wrappers/commit/bd0fa42705393cb1408a84ce4a060272d5428ce6)) * autobump bio/gatk/learnreadorientationmodel ([#1653](https://www.github.com/snakemake/snakemake-wrappers/issues/1653)) ([c2c64ea](https://www.github.com/snakemake/snakemake-wrappers/commit/c2c64ea596f00ccb67b27aa38c94c9a5376e172d)) * autobump bio/gatk/leftalignandtrimvariants ([#1639](https://www.github.com/snakemake/snakemake-wrappers/issues/1639)) ([c3f89ea](https://www.github.com/snakemake/snakemake-wrappers/commit/c3f89ea03d5bd6438d4af260c1c1c6f906a95926)) * autobump bio/gatk/leftalignandtrimvariants ([#1697](https://www.github.com/snakemake/snakemake-wrappers/issues/1697)) ([c4b738a](https://www.github.com/snakemake/snakemake-wrappers/commit/c4b738a40d21b0f14dd52b9e112ec88233b9f71b)) * autobump bio/gatk/markduplicatesspark ([#1467](https://www.github.com/snakemake/snakemake-wrappers/issues/1467)) ([1d383b7](https://www.github.com/snakemake/snakemake-wrappers/commit/1d383b71d42a13ba2df6a9404bb7d10ecbcc4b6b)) * autobump bio/gatk/modelsegments ([#1543](https://www.github.com/snakemake/snakemake-wrappers/issues/1543)) ([f26ea4a](https://www.github.com/snakemake/snakemake-wrappers/commit/f26ea4a8d1090467d3b5c2785cde878b2b58ba82)) * autobump bio/gatk/modelsegments ([#1611](https://www.github.com/snakemake/snakemake-wrappers/issues/1611)) ([77ff014](https://www.github.com/snakemake/snakemake-wrappers/commit/77ff01495e7dc8df19b11d6acbff6ae1e98ab474)) * autobump bio/gatk/mutect ([#1526](https://www.github.com/snakemake/snakemake-wrappers/issues/1526)) ([4789991](https://www.github.com/snakemake/snakemake-wrappers/commit/4789991a17450c2c36681ceeeb53d265fadf6b5f)) * autobump bio/gatk/mutect ([#1696](https://www.github.com/snakemake/snakemake-wrappers/issues/1696)) ([666ba69](https://www.github.com/snakemake/snakemake-wrappers/commit/666ba698538fab13afbb9b52a01e1abc8343f76a)) * autobump bio/gatk/printreadsspark ([#1699](https://www.github.com/snakemake/snakemake-wrappers/issues/1699)) ([1aee674](https://www.github.com/snakemake/snakemake-wrappers/commit/1aee674a645953d056548fd38dad966606b7d185)) * autobump bio/gatk/scatterintervalsbyns ([#1597](https://www.github.com/snakemake/snakemake-wrappers/issues/1597)) ([214c231](https://www.github.com/snakemake/snakemake-wrappers/commit/214c2316448fff942c7824f14cf754212d71c554)) * autobump bio/gatk/scatterintervalsbyns ([#1682](https://www.github.com/snakemake/snakemake-wrappers/issues/1682)) ([42e0238](https://www.github.com/snakemake/snakemake-wrappers/commit/42e0238a57d4acf8ec76eba77f8197ddc7e154db)) * autobump bio/gatk/selectvariants ([#1695](https://www.github.com/snakemake/snakemake-wrappers/issues/1695)) ([fb5b42d](https://www.github.com/snakemake/snakemake-wrappers/commit/fb5b42d01674337805b741a2e64c340204f09f19)) * autobump bio/gatk/splitintervals ([#1591](https://www.github.com/snakemake/snakemake-wrappers/issues/1591)) ([67ccba6](https://www.github.com/snakemake/snakemake-wrappers/commit/67ccba699188b4c02dd0bf2cb1f2557fcf5a544c)) * autobump bio/gatk/splitncigarreads ([#1536](https://www.github.com/snakemake/snakemake-wrappers/issues/1536)) ([68b02fe](https://www.github.com/snakemake/snakemake-wrappers/commit/68b02fe81e886721ac457895823491a4eaf21c9d)) * autobump bio/gatk/splitncigarreads ([#1562](https://www.github.com/snakemake/snakemake-wrappers/issues/1562)) ([c27f4a6](https://www.github.com/snakemake/snakemake-wrappers/commit/c27f4a6a224de88d1bb6855af5643c84e485385e)) * autobump bio/gatk/variantannotator ([#1582](https://www.github.com/snakemake/snakemake-wrappers/issues/1582)) ([2b41efe](https://www.github.com/snakemake/snakemake-wrappers/commit/2b41efeea999b2408cd58afb21eb9fa04cff7e42)) * autobump bio/gatk/varianteval ([#1545](https://www.github.com/snakemake/snakemake-wrappers/issues/1545)) ([1b70868](https://www.github.com/snakemake/snakemake-wrappers/commit/1b708687cbf5235cda3ba23c3ccaed1075394f88)) * autobump bio/gatk/varianteval ([#1619](https://www.github.com/snakemake/snakemake-wrappers/issues/1619)) ([78c57d1](https://www.github.com/snakemake/snakemake-wrappers/commit/78c57d16fccb06acb46c36707cae8beb43b8e68f)) * autobump bio/gatk/varianteval ([#1677](https://www.github.com/snakemake/snakemake-wrappers/issues/1677)) ([29eb05c](https://www.github.com/snakemake/snakemake-wrappers/commit/29eb05c8736207cd37ce620d9b43863e5f4ae3a2)) * autobump bio/gatk/variantfiltration ([#1577](https://www.github.com/snakemake/snakemake-wrappers/issues/1577)) ([0dabdf1](https://www.github.com/snakemake/snakemake-wrappers/commit/0dabdf194ead2950b1c2122cf304541f3da83e96)) * autobump bio/gatk/variantstotable ([#1539](https://www.github.com/snakemake/snakemake-wrappers/issues/1539)) ([00d5abd](https://www.github.com/snakemake/snakemake-wrappers/commit/00d5abd3d567688fb380da00358ad148f76b4f6b)) * autobump bio/gatk/variantstotable ([#1559](https://www.github.com/snakemake/snakemake-wrappers/issues/1559)) ([eba4873](https://www.github.com/snakemake/snakemake-wrappers/commit/eba48737c41efad2b63f77fa9f37c9ee3e308ed9)) * autobump bio/gatk3/baserecalibrator ([#1642](https://www.github.com/snakemake/snakemake-wrappers/issues/1642)) ([782593d](https://www.github.com/snakemake/snakemake-wrappers/commit/782593d339d4d51a59d52048e53d7af5929b23c7)) * autobump bio/gatk3/indelrealigner ([#1636](https://www.github.com/snakemake/snakemake-wrappers/issues/1636)) ([ab6be44](https://www.github.com/snakemake/snakemake-wrappers/commit/ab6be44365616650342ad7650075fc052bb2a609)) * autobump bio/gatk3/realignertargetcreator ([#1587](https://www.github.com/snakemake/snakemake-wrappers/issues/1587)) ([1e320ac](https://www.github.com/snakemake/snakemake-wrappers/commit/1e320acb33840a6e875b908bc4cd93d3910707f4)) * autobump bio/gatk3/realignertargetcreator ([#1650](https://www.github.com/snakemake/snakemake-wrappers/issues/1650)) ([66bfa88](https://www.github.com/snakemake/snakemake-wrappers/commit/66bfa88b02b68d6d853d934c6ff596be3d01f149)) * autobump bio/gdc-api/bam-slicing ([#1552](https://www.github.com/snakemake/snakemake-wrappers/issues/1552)) ([9760140](https://www.github.com/snakemake/snakemake-wrappers/commit/9760140b9a0c058c44c23ba95b3ef59d15e35473)) * autobump bio/gdc-api/bam-slicing ([#1627](https://www.github.com/snakemake/snakemake-wrappers/issues/1627)) ([14ff838](https://www.github.com/snakemake/snakemake-wrappers/commit/14ff8382dfbb04ffcff2e1a287317b45e93789b0)) * autobump bio/genomepy ([#1542](https://www.github.com/snakemake/snakemake-wrappers/issues/1542)) ([f615808](https://www.github.com/snakemake/snakemake-wrappers/commit/f6158084badc5b42a1eae0f71b66c45568e01cf3)) * autobump bio/hifiasm ([#1672](https://www.github.com/snakemake/snakemake-wrappers/issues/1672)) ([7ad6d77](https://www.github.com/snakemake/snakemake-wrappers/commit/7ad6d7797895488cc792c1ddfbaedabcf68e6b3f)) * autobump bio/hifiasm ([#1694](https://www.github.com/snakemake/snakemake-wrappers/issues/1694)) ([a99f0ef](https://www.github.com/snakemake/snakemake-wrappers/commit/a99f0ef10d75e69092973f6e152a4ab4fe2d2630)) * autobump bio/jannovar ([#1640](https://www.github.com/snakemake/snakemake-wrappers/issues/1640)) ([cf6d9d4](https://www.github.com/snakemake/snakemake-wrappers/commit/cf6d9d416bd170ee170a878ce3b33eaf64eacfc5)) * autobump bio/kallisto/index ([#1708](https://www.github.com/snakemake/snakemake-wrappers/issues/1708)) ([a84c0ab](https://www.github.com/snakemake/snakemake-wrappers/commit/a84c0ab498df5916c7017879394bb183e05ed450)) * autobump bio/kallisto/quant ([#1629](https://www.github.com/snakemake/snakemake-wrappers/issues/1629)) ([d076334](https://www.github.com/snakemake/snakemake-wrappers/commit/d076334515e77aa6efb7fa1f415fd7f8b9433a8c)) * autobump bio/last/lastal ([#1666](https://www.github.com/snakemake/snakemake-wrappers/issues/1666)) ([1aababe](https://www.github.com/snakemake/snakemake-wrappers/commit/1aababe757430337259293564e202190ad5eedd3)) * autobump bio/last/lastal ([#1709](https://www.github.com/snakemake/snakemake-wrappers/issues/1709)) ([fa7a100](https://www.github.com/snakemake/snakemake-wrappers/commit/fa7a10041c5276314a254d671a304f6c8851a0db)) * autobump bio/macs2/callpeak ([#1662](https://www.github.com/snakemake/snakemake-wrappers/issues/1662)) ([e175ce2](https://www.github.com/snakemake/snakemake-wrappers/commit/e175ce27e13b190e0bb27b37ab8f51cc06ed41d3)) * autobump bio/mashmap ([#1474](https://www.github.com/snakemake/snakemake-wrappers/issues/1474)) ([bf67fcd](https://www.github.com/snakemake/snakemake-wrappers/commit/bf67fcd92ae83269007e656664c7fa8be6b757f0)) * autobump bio/minimap2/aligner ([#1592](https://www.github.com/snakemake/snakemake-wrappers/issues/1592)) ([c2c611c](https://www.github.com/snakemake/snakemake-wrappers/commit/c2c611ca968f3bb03e69f4cfca40636c0a278a6c)) * autobump bio/mosdepth ([#1720](https://www.github.com/snakemake/snakemake-wrappers/issues/1720)) ([828f780](https://www.github.com/snakemake/snakemake-wrappers/commit/828f780d44b40f89de3ff278ff9d64fc6455eb1e)) * autobump bio/nonpareil/infer ([#1606](https://www.github.com/snakemake/snakemake-wrappers/issues/1606)) ([a19604d](https://www.github.com/snakemake/snakemake-wrappers/commit/a19604d729dc45c2d7b124512dc5219ef44ec261)) * autobump bio/nonpareil/infer ([#1681](https://www.github.com/snakemake/snakemake-wrappers/issues/1681)) ([e81c291](https://www.github.com/snakemake/snakemake-wrappers/commit/e81c291494d7eabc0e8384dc83831f614cca2439)) * autobump bio/nonpareil/infer ([#1701](https://www.github.com/snakemake/snakemake-wrappers/issues/1701)) ([0fa0b21](https://www.github.com/snakemake/snakemake-wrappers/commit/0fa0b2120ae4f7300eb94a2cbbf88c63fd970abf)) * autobump bio/open-cravat/module ([#1664](https://www.github.com/snakemake/snakemake-wrappers/issues/1664)) ([58047f7](https://www.github.com/snakemake/snakemake-wrappers/commit/58047f710ae8ea7e76e701c3f27f05b3b5c256d0)) * autobump bio/open-cravat/run ([#1596](https://www.github.com/snakemake/snakemake-wrappers/issues/1596)) ([acdb91e](https://www.github.com/snakemake/snakemake-wrappers/commit/acdb91ec328d5d8f27be985409fc769a1d0e45ad)) * autobump bio/pbmm2/align ([#1553](https://www.github.com/snakemake/snakemake-wrappers/issues/1553)) ([03be953](https://www.github.com/snakemake/snakemake-wrappers/commit/03be95318516cecd6b69424e245200bd8280acfb)) * autobump bio/picard/addorreplacereadgroups ([#1571](https://www.github.com/snakemake/snakemake-wrappers/issues/1571)) ([a68069e](https://www.github.com/snakemake/snakemake-wrappers/commit/a68069ed69bf618385e36f2eb4d1decc55b93115)) * autobump bio/picard/collectalignmentsummarymetrics ([#1716](https://www.github.com/snakemake/snakemake-wrappers/issues/1716)) ([f10e617](https://www.github.com/snakemake/snakemake-wrappers/commit/f10e617b8d5706a7913abb8ccb04e2d38531026d)) * autobump bio/picard/collectgcbiasmetrics ([#1660](https://www.github.com/snakemake/snakemake-wrappers/issues/1660)) ([aa83b56](https://www.github.com/snakemake/snakemake-wrappers/commit/aa83b567dc9f37254f00e802dea60551c2f9bac3)) * autobump bio/picard/collecthsmetrics ([#1565](https://www.github.com/snakemake/snakemake-wrappers/issues/1565)) ([58ebb45](https://www.github.com/snakemake/snakemake-wrappers/commit/58ebb45b750782fc968535475b96755b366c712d)) * autobump bio/picard/collectinsertsizemetrics ([#1616](https://www.github.com/snakemake/snakemake-wrappers/issues/1616)) ([83bbae5](https://www.github.com/snakemake/snakemake-wrappers/commit/83bbae58963ae7d7affa6864bbd0c3aa390f3274)) * autobump bio/picard/collectmultiplemetrics ([#1533](https://www.github.com/snakemake/snakemake-wrappers/issues/1533)) ([6163ba6](https://www.github.com/snakemake/snakemake-wrappers/commit/6163ba6c78980e85111a107e4a066659933557cf)) * autobump bio/picard/collectmultiplemetrics ([#1579](https://www.github.com/snakemake/snakemake-wrappers/issues/1579)) ([0009a9b](https://www.github.com/snakemake/snakemake-wrappers/commit/0009a9bddd279f9ad214ca59d93d8b39006fc850)) * autobump bio/picard/collectrnaseqmetrics ([#1567](https://www.github.com/snakemake/snakemake-wrappers/issues/1567)) ([8d6a569](https://www.github.com/snakemake/snakemake-wrappers/commit/8d6a5694ed861ab9edb00ee135767102174e8cd7)) * autobump bio/picard/collecttargetedpcrmetrics ([#1584](https://www.github.com/snakemake/snakemake-wrappers/issues/1584)) ([60c1626](https://www.github.com/snakemake/snakemake-wrappers/commit/60c1626eee96437f9b775f9de2cd5d15a9805923)) * autobump bio/picard/createsequencedictionary ([#1643](https://www.github.com/snakemake/snakemake-wrappers/issues/1643)) ([ddb979d](https://www.github.com/snakemake/snakemake-wrappers/commit/ddb979d72f7720ee554ad44d05d66957aad2b275)) * autobump bio/picard/mergesamfiles ([#1690](https://www.github.com/snakemake/snakemake-wrappers/issues/1690)) ([cf90f0d](https://www.github.com/snakemake/snakemake-wrappers/commit/cf90f0d07c802d7071724acfc4667fb80a7b28f8)) * autobump bio/picard/mergevcfs ([#1718](https://www.github.com/snakemake/snakemake-wrappers/issues/1718)) ([4681800](https://www.github.com/snakemake/snakemake-wrappers/commit/46818001763bea35a99e34d5d76cdb8a5c63995d)) * autobump bio/picard/revertsam ([#1580](https://www.github.com/snakemake/snakemake-wrappers/issues/1580)) ([8c9aa09](https://www.github.com/snakemake/snakemake-wrappers/commit/8c9aa090857328b1c53d41c29d817fd2e30fd3ba)) * autobump bio/picard/samtofastq ([#1569](https://www.github.com/snakemake/snakemake-wrappers/issues/1569)) ([9157dea](https://www.github.com/snakemake/snakemake-wrappers/commit/9157deaa1f89de327d4efbd797bf1173dbd9ec69)) * autobump bio/picard/sortsam ([#1530](https://www.github.com/snakemake/snakemake-wrappers/issues/1530)) ([075a64f](https://www.github.com/snakemake/snakemake-wrappers/commit/075a64fcccb9cc8ed9202fb081c96b35afd19c99)) * autobump bio/pretext/map ([#1721](https://www.github.com/snakemake/snakemake-wrappers/issues/1721)) ([b13f290](https://www.github.com/snakemake/snakemake-wrappers/commit/b13f290058329c7cbc5dbe2ca3f32271c802adb2)) * autobump bio/pyroe/makesplicedintronic ([#1564](https://www.github.com/snakemake/snakemake-wrappers/issues/1564)) ([de214c6](https://www.github.com/snakemake/snakemake-wrappers/commit/de214c69c156f60579bd7c8f20ef9b1b289572e8)) * autobump bio/pyroe/makeunspliceunspliced ([#1566](https://www.github.com/snakemake/snakemake-wrappers/issues/1566)) ([422e811](https://www.github.com/snakemake/snakemake-wrappers/commit/422e8112ca1cf98fbc30e01faf5300622862b7f3)) * autobump bio/qualimap/bamqc ([#1621](https://www.github.com/snakemake/snakemake-wrappers/issues/1621)) ([6806b8a](https://www.github.com/snakemake/snakemake-wrappers/commit/6806b8ae9f34315322bbfe50a5e9a81ac1718337)) * autobump bio/salmon/index ([#1532](https://www.github.com/snakemake/snakemake-wrappers/issues/1532)) ([dad1a25](https://www.github.com/snakemake/snakemake-wrappers/commit/dad1a25a858933902b0c7fba3fcbef51fd540723)) * autobump bio/samtools/calmd ([#1576](https://www.github.com/snakemake/snakemake-wrappers/issues/1576)) ([76c7661](https://www.github.com/snakemake/snakemake-wrappers/commit/76c76614bbd715396f19c38d32b38d8f489b4e84)) * autobump bio/samtools/faidx ([#1698](https://www.github.com/snakemake/snakemake-wrappers/issues/1698)) ([665c9c4](https://www.github.com/snakemake/snakemake-wrappers/commit/665c9c4dc375c4c1268703c865e99c047c061252)) * autobump bio/samtools/fastx ([#1644](https://www.github.com/snakemake/snakemake-wrappers/issues/1644)) ([26fef49](https://www.github.com/snakemake/snakemake-wrappers/commit/26fef493665b6cafd1a01cc61f062bee10a3c77d)) * autobump bio/samtools/fixmate ([#1686](https://www.github.com/snakemake/snakemake-wrappers/issues/1686)) ([3de2261](https://www.github.com/snakemake/snakemake-wrappers/commit/3de2261f9139a451b226f989e499f9b4062b8430)) * autobump bio/samtools/flagstat ([#1612](https://www.github.com/snakemake/snakemake-wrappers/issues/1612)) ([85c89a1](https://www.github.com/snakemake/snakemake-wrappers/commit/85c89a17b64010ed54035699cf2fef145ccd9699)) * autobump bio/samtools/sort ([#1528](https://www.github.com/snakemake/snakemake-wrappers/issues/1528)) ([11453ad](https://www.github.com/snakemake/snakemake-wrappers/commit/11453ad0b0dbd7b20efabaf5bb0050210ff3b95f)) * autobump bio/samtools/sort ([#1707](https://www.github.com/snakemake/snakemake-wrappers/issues/1707)) ([2a9efe5](https://www.github.com/snakemake/snakemake-wrappers/commit/2a9efe5956a6b5eecd9bdc6069f1e17e59e0a5f8)) * autobump bio/samtools/stats ([#1615](https://www.github.com/snakemake/snakemake-wrappers/issues/1615)) ([6b1bb79](https://www.github.com/snakemake/snakemake-wrappers/commit/6b1bb79c5c28c40ec2d62abc0543c0961ffa216d)) * autobump bio/samtools/stats ([#1628](https://www.github.com/snakemake/snakemake-wrappers/issues/1628)) ([6895834](https://www.github.com/snakemake/snakemake-wrappers/commit/689583407979460b92e3c2c581b7695a35ddab3d)) * autobump bio/samtools/stats ([#1674](https://www.github.com/snakemake/snakemake-wrappers/issues/1674)) ([7bd8a71](https://www.github.com/snakemake/snakemake-wrappers/commit/7bd8a718156c2c73ca4228324132ca3527a6ffab)) * autobump bio/samtools/view ([#1525](https://www.github.com/snakemake/snakemake-wrappers/issues/1525)) ([2755074](https://www.github.com/snakemake/snakemake-wrappers/commit/275507412b0d4a6769080a8b8e78e0f6a6776c22)) * autobump bio/samtools/view ([#1608](https://www.github.com/snakemake/snakemake-wrappers/issues/1608)) ([f582deb](https://www.github.com/snakemake/snakemake-wrappers/commit/f582deb36f56a10d2c1e6c2d789229a987493c01)) * autobump bio/seqkit ([#1610](https://www.github.com/snakemake/snakemake-wrappers/issues/1610)) ([cabdc5a](https://www.github.com/snakemake/snakemake-wrappers/commit/cabdc5a900ec70fbd6f0316e983d9905c354d306)) * autobump bio/seqkit ([#1673](https://www.github.com/snakemake/snakemake-wrappers/issues/1673)) ([13261f8](https://www.github.com/snakemake/snakemake-wrappers/commit/13261f8391c4834dd6dcc689839201eed9006d1a)) * autobump bio/seqtk/mergepe ([#1585](https://www.github.com/snakemake/snakemake-wrappers/issues/1585)) ([c671e66](https://www.github.com/snakemake/snakemake-wrappers/commit/c671e667ca0db03072aa562cff7bef1bfc9577f5)) * autobump bio/snpeff/annotate ([#1624](https://www.github.com/snakemake/snakemake-wrappers/issues/1624)) ([34a1005](https://www.github.com/snakemake/snakemake-wrappers/commit/34a1005b6e5f539428f0d4e409f5f98db4b9afce)) * autobump bio/snpeff/annotate ([#1685](https://www.github.com/snakemake/snakemake-wrappers/issues/1685)) ([a7b797d](https://www.github.com/snakemake/snakemake-wrappers/commit/a7b797d0860cd336de1805660279e6561217097b)) * autobump bio/snpeff/download ([#1626](https://www.github.com/snakemake/snakemake-wrappers/issues/1626)) ([9a649d3](https://www.github.com/snakemake/snakemake-wrappers/commit/9a649d3999b36de89f3ca4311a210f87af31790e)) * autobump bio/snpsift/annotate ([#1593](https://www.github.com/snakemake/snakemake-wrappers/issues/1593)) ([bc9c1a6](https://www.github.com/snakemake/snakemake-wrappers/commit/bc9c1a6bde205599beecadd67145a5f61b669e39)) * autobump bio/snpsift/annotate ([#1645](https://www.github.com/snakemake/snakemake-wrappers/issues/1645)) ([be76f44](https://www.github.com/snakemake/snakemake-wrappers/commit/be76f44e1cd80653468744511671bce1fd902774)) * autobump bio/snpsift/annotate ([#1675](https://www.github.com/snakemake/snakemake-wrappers/issues/1675)) ([baee34b](https://www.github.com/snakemake/snakemake-wrappers/commit/baee34b54edc532bf4201a7879ed0e6be5e31733)) * autobump bio/snpsift/gwascat ([#1613](https://www.github.com/snakemake/snakemake-wrappers/issues/1613)) ([1764ca5](https://www.github.com/snakemake/snakemake-wrappers/commit/1764ca5869b8e1625b12e5879a011f0731e10f55)) * autobump bio/snpsift/gwascat ([#1657](https://www.github.com/snakemake/snakemake-wrappers/issues/1657)) ([8cc8988](https://www.github.com/snakemake/snakemake-wrappers/commit/8cc8988f04b9817658328e0dbe675ce48d3e7d7e)) * autobump bio/snpsift/varType ([#1583](https://www.github.com/snakemake/snakemake-wrappers/issues/1583)) ([ad5d062](https://www.github.com/snakemake/snakemake-wrappers/commit/ad5d062fdc333fbe88c0108d9d77bb5327d7b421)) * autobump bio/sra-tools/fasterq-dump ([#1655](https://www.github.com/snakemake/snakemake-wrappers/issues/1655)) ([ceb9ed8](https://www.github.com/snakemake/snakemake-wrappers/commit/ceb9ed8f9eba541b7b6c8464dbd7a1323c0c495c)) * autobump bio/tabix/index ([#1658](https://www.github.com/snakemake/snakemake-wrappers/issues/1658)) ([3bcd66d](https://www.github.com/snakemake/snakemake-wrappers/commit/3bcd66d900b786f3dcdbdaf40880b96e08df58c7)) * autobump bio/transdecoder/longorfs ([#1617](https://www.github.com/snakemake/snakemake-wrappers/issues/1617)) ([39bb6fc](https://www.github.com/snakemake/snakemake-wrappers/commit/39bb6fc9359d003760b0b92f83df5f911272462b)) * autobump bio/transdecoder/predict ([#1568](https://www.github.com/snakemake/snakemake-wrappers/issues/1568)) ([1d19059](https://www.github.com/snakemake/snakemake-wrappers/commit/1d190599e05ef242eba2a415d42720a959b9b46c)) * autobump bio/tximport ([#1632](https://www.github.com/snakemake/snakemake-wrappers/issues/1632)) ([bbbb631](https://www.github.com/snakemake/snakemake-wrappers/commit/bbbb63132b172359877c3b292444320bdc977eed)) * autobump bio/varscan/mpileup2indel ([#1556](https://www.github.com/snakemake/snakemake-wrappers/issues/1556)) ([5d4f281](https://www.github.com/snakemake/snakemake-wrappers/commit/5d4f2810968c4d59caf657233c9a2a2648713ffd)) * autobump bio/varscan/mpileup2snp ([#1665](https://www.github.com/snakemake/snakemake-wrappers/issues/1665)) ([4171043](https://www.github.com/snakemake/snakemake-wrappers/commit/41710437367100bec97330c3cce0f5211c0f34e2)) * autobump bio/varscan/somatic ([#1598](https://www.github.com/snakemake/snakemake-wrappers/issues/1598)) ([0a86cbc](https://www.github.com/snakemake/snakemake-wrappers/commit/0a86cbc2bb20b86c9c8138ecf6df2a0addca5ea3)) * autobump bio/vembrane/filter ([#1623](https://www.github.com/snakemake/snakemake-wrappers/issues/1623)) ([47e6d58](https://www.github.com/snakemake/snakemake-wrappers/commit/47e6d5864002b7ab3162b2687b5b1da66187b0e6)) * autobump bio/vembrane/table ([#1605](https://www.github.com/snakemake/snakemake-wrappers/issues/1605)) ([9c616da](https://www.github.com/snakemake/snakemake-wrappers/commit/9c616daa55ee34376e9ad19873ff47e23588c4c1)) * autobump bio/vep/cache ([#1604](https://www.github.com/snakemake/snakemake-wrappers/issues/1604)) ([1681978](https://www.github.com/snakemake/snakemake-wrappers/commit/16819786ffbd6c7d7a54bddaa3fadb481c4d018e)) * autobump bio/vg/construct ([#1529](https://www.github.com/snakemake/snakemake-wrappers/issues/1529)) ([6206f18](https://www.github.com/snakemake/snakemake-wrappers/commit/6206f18136d322026075e3796cad486852c62a92)) * autobump bio/vg/sim ([#1573](https://www.github.com/snakemake/snakemake-wrappers/issues/1573)) ([7c2b587](https://www.github.com/snakemake/snakemake-wrappers/commit/7c2b587409dbaf75ae29984b8059e4e3d2402ba0)) * autobump bio/vsearch ([#1590](https://www.github.com/snakemake/snakemake-wrappers/issues/1590)) ([ed2e49b](https://www.github.com/snakemake/snakemake-wrappers/commit/ed2e49b6aed0a0a1f5d5a6613b66aea067e0ef94)) * autobump bio/vsearch ([#1700](https://www.github.com/snakemake/snakemake-wrappers/issues/1700)) ([92f42fc](https://www.github.com/snakemake/snakemake-wrappers/commit/92f42fcfe28e06ecfab070c8539d096fb2aff3a0)) * autobump utils/datavzrd ([#1538](https://www.github.com/snakemake/snakemake-wrappers/issues/1538)) ([10a6b0b](https://www.github.com/snakemake/snakemake-wrappers/commit/10a6b0b47943544ebfa291e759390ffa933a7624)) * autobump utils/datavzrd ([#1717](https://www.github.com/snakemake/snakemake-wrappers/issues/1717)) ([3ab8832](https://www.github.com/snakemake/snakemake-wrappers/commit/3ab88327c5581bb9809bf7a918011db53ce0d159)) * set version for coolpuppy and update versions for some cooltools wrappers ([#1546](https://www.github.com/snakemake/snakemake-wrappers/issues/1546)) ([41ef6d0](https://www.github.com/snakemake/snakemake-wrappers/commit/41ef6d0573daad70e4edd1601dcca29a9ceba801)) --- 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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Description
This meta-wrapper simply aligns, filters and deduplicates reads. I've been helping co-workers with Snakemake basics and snakemake-wrappers, and I used this very short pipeline.
QC
For all wrappers added by this PR,
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),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,