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fix: account for memory overhead #2648
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dlaehnemann
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Feb 22, 2024
dlaehnemann
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Feb 22, 2024
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Good catch and clean fix, with proper linkout. Many thanks.
johanneskoester
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Feb 27, 2024
🤖 I have created a release \*beep\* \*boop\* --- ### [3.3.7](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.3.6...v3.3.7) (2024-02-27) ### Bug Fixes * account for memory overhead ([#2648](https://www.github.com/snakemake/snakemake-wrappers/issues/2648)) ([6a05aad](https://www.github.com/snakemake/snakemake-wrappers/commit/6a05aad6066b0f3aadb92e1f7f931c161222b150)) ### Performance Improvements * autobump bio/bbtools ([#2627](https://www.github.com/snakemake/snakemake-wrappers/issues/2627)) ([7f5b520](https://www.github.com/snakemake/snakemake-wrappers/commit/7f5b5209923401ec20fd1a08063821767300b40a)) * autobump bio/diamond/blastp ([#2630](https://www.github.com/snakemake/snakemake-wrappers/issues/2630)) ([3911776](https://www.github.com/snakemake/snakemake-wrappers/commit/39117768d8978f51fade713abf843d970f98c623)) * autobump bio/diamond/blastx ([#2629](https://www.github.com/snakemake/snakemake-wrappers/issues/2629)) ([faf5de8](https://www.github.com/snakemake/snakemake-wrappers/commit/faf5de8da5579e97620f668b6f6ac63dc57cc0b4)) * autobump bio/diamond/makedb ([#2628](https://www.github.com/snakemake/snakemake-wrappers/issues/2628)) ([7ddca67](https://www.github.com/snakemake/snakemake-wrappers/commit/7ddca679c07cc79598f4099ba0f17d3f10a4247f)) * autobump bio/encode_fastq_downloader ([#2682](https://www.github.com/snakemake/snakemake-wrappers/issues/2682)) ([eb4a093](https://www.github.com/snakemake/snakemake-wrappers/commit/eb4a0939a1c6de100d1c1689d8cbb32402c8d328)) * autobump bio/fgbio/collectduplexseqmetrics ([#2631](https://www.github.com/snakemake/snakemake-wrappers/issues/2631)) ([7a58ee9](https://www.github.com/snakemake/snakemake-wrappers/commit/7a58ee99d23d1f75024bf2e12cb82c3e99bdeefc)) * autobump bio/galah ([#2670](https://www.github.com/snakemake/snakemake-wrappers/issues/2670)) ([8972be1](https://www.github.com/snakemake/snakemake-wrappers/commit/8972be1d8625cd2a359088fb41bdec0945030a9e)) * autobump bio/gatk/applybqsr ([#2662](https://www.github.com/snakemake/snakemake-wrappers/issues/2662)) ([2d1ff8e](https://www.github.com/snakemake/snakemake-wrappers/commit/2d1ff8eeb36fd82f33e03149f2205cc795993f85)) * autobump bio/gatk/applybqsrspark ([#2669](https://www.github.com/snakemake/snakemake-wrappers/issues/2669)) ([46a8acd](https://www.github.com/snakemake/snakemake-wrappers/commit/46a8acdff97cef5ff1e064ccedac90ba05659bb6)) * autobump bio/gatk/baserecalibratorspark ([#2651](https://www.github.com/snakemake/snakemake-wrappers/issues/2651)) ([3b4f517](https://www.github.com/snakemake/snakemake-wrappers/commit/3b4f51740d2a5b371789385fbd0ffe307af100f5)) * autobump bio/gatk/calculatecontamination ([#2673](https://www.github.com/snakemake/snakemake-wrappers/issues/2673)) ([056c9a0](https://www.github.com/snakemake/snakemake-wrappers/commit/056c9a0cb2f9198a700c1972d0ab7879a7178cdf)) * autobump bio/gatk/callcopyratiosegments ([#2655](https://www.github.com/snakemake/snakemake-wrappers/issues/2655)) ([b1932ae](https://www.github.com/snakemake/snakemake-wrappers/commit/b1932ae110fd9e52b7a4c782ed72c98636a84fc0)) * autobump bio/gatk/cleansam ([#2660](https://www.github.com/snakemake/snakemake-wrappers/issues/2660)) ([3802099](https://www.github.com/snakemake/snakemake-wrappers/commit/3802099d38708052cef5284bb3ec93d64e362f58)) * autobump bio/gatk/collectreadcounts ([#2666](https://www.github.com/snakemake/snakemake-wrappers/issues/2666)) ([0aa2cce](https://www.github.com/snakemake/snakemake-wrappers/commit/0aa2ccee2a6b763dc4fe83da11ed9827276b34a5)) * autobump bio/gatk/combinegvcfs ([#2686](https://www.github.com/snakemake/snakemake-wrappers/issues/2686)) ([a903745](https://www.github.com/snakemake/snakemake-wrappers/commit/a903745748b38685cfa5c6381abdcfbfce80803e)) * autobump bio/gatk/denoisereadcounts ([#2685](https://www.github.com/snakemake/snakemake-wrappers/issues/2685)) ([1e8498b](https://www.github.com/snakemake/snakemake-wrappers/commit/1e8498b5c7771ea2f7c360abeb640e6caa665db4)) * autobump bio/gatk/depthofcoverage ([#2658](https://www.github.com/snakemake/snakemake-wrappers/issues/2658)) ([1f43492](https://www.github.com/snakemake/snakemake-wrappers/commit/1f434923e7d4c0cc2905b3f6f17e1735577e8631)) * autobump bio/gatk/estimatelibrarycomplexity ([#2650](https://www.github.com/snakemake/snakemake-wrappers/issues/2650)) ([e9395ff](https://www.github.com/snakemake/snakemake-wrappers/commit/e9395ff31acaa58506258905f62582f9db0a55c0)) * autobump bio/gatk/filtermutectcalls ([#2684](https://www.github.com/snakemake/snakemake-wrappers/issues/2684)) ([b239e62](https://www.github.com/snakemake/snakemake-wrappers/commit/b239e62c5d0d67b138d9af77d8318db9e62dd9af)) * autobump bio/gatk/genomicsdbimport ([#2665](https://www.github.com/snakemake/snakemake-wrappers/issues/2665)) ([a38b278](https://www.github.com/snakemake/snakemake-wrappers/commit/a38b278adbb28857b59d25c0acca53daf6e2478f)) * autobump bio/gatk/getpileupsummaries ([#2657](https://www.github.com/snakemake/snakemake-wrappers/issues/2657)) ([7523193](https://www.github.com/snakemake/snakemake-wrappers/commit/75231932739bd97c39814a4b819c119288b6bddb)) * autobump bio/gatk/learnreadorientationmodel ([#2653](https://www.github.com/snakemake/snakemake-wrappers/issues/2653)) ([773e78c](https://www.github.com/snakemake/snakemake-wrappers/commit/773e78c49e9c4f70291f2a98d99852fe347bc244)) * autobump bio/gatk/leftalignandtrimvariants ([#2656](https://www.github.com/snakemake/snakemake-wrappers/issues/2656)) ([183950c](https://www.github.com/snakemake/snakemake-wrappers/commit/183950c6424d223915bca50deba31d5c3423d385)) * autobump bio/gatk/markduplicatesspark ([#2659](https://www.github.com/snakemake/snakemake-wrappers/issues/2659)) ([706cda3](https://www.github.com/snakemake/snakemake-wrappers/commit/706cda3432a12b4a7379edc4f146b2d29919535a)) * autobump bio/gatk/modelsegments ([#2663](https://www.github.com/snakemake/snakemake-wrappers/issues/2663)) ([bc40698](https://www.github.com/snakemake/snakemake-wrappers/commit/bc40698b6a902012a6a1e197eccfd58ec40d7910)) * autobump bio/gatk/mutect ([#2661](https://www.github.com/snakemake/snakemake-wrappers/issues/2661)) ([0e1d98a](https://www.github.com/snakemake/snakemake-wrappers/commit/0e1d98a96fe448279f38e31b871acf2abf5ca47e)) * autobump bio/gatk/scatterintervalsbyns ([#2674](https://www.github.com/snakemake/snakemake-wrappers/issues/2674)) ([e49b027](https://www.github.com/snakemake/snakemake-wrappers/commit/e49b0273bce205a3597ac2709e599c1ce1f18317)) * autobump bio/gatk/splitintervals ([#2667](https://www.github.com/snakemake/snakemake-wrappers/issues/2667)) ([332eed5](https://www.github.com/snakemake/snakemake-wrappers/commit/332eed549c82ef34d150da68e6af5dfd534ae467)) * autobump bio/gatk/splitncigarreads ([#2672](https://www.github.com/snakemake/snakemake-wrappers/issues/2672)) ([dabbc1e](https://www.github.com/snakemake/snakemake-wrappers/commit/dabbc1eec0f5805664a83d08f603a0dcd91407da)) * autobump bio/gatk/variantannotator ([#2664](https://www.github.com/snakemake/snakemake-wrappers/issues/2664)) ([2142589](https://www.github.com/snakemake/snakemake-wrappers/commit/21425891baf75967a8d6c1bb373168ce4e4bec4d)) * autobump bio/gatk/varianteval ([#2654](https://www.github.com/snakemake/snakemake-wrappers/issues/2654)) ([9d4ffea](https://www.github.com/snakemake/snakemake-wrappers/commit/9d4ffea301af15a5829d4f04b649431139475bc8)) * autobump bio/gatk/variantfiltration ([#2668](https://www.github.com/snakemake/snakemake-wrappers/issues/2668)) ([5cf5407](https://www.github.com/snakemake/snakemake-wrappers/commit/5cf54078192852b3de6f853c0a5fff0176dfbae0)) * autobump bio/gatk/variantrecalibrator ([#2652](https://www.github.com/snakemake/snakemake-wrappers/issues/2652)) ([714ae91](https://www.github.com/snakemake/snakemake-wrappers/commit/714ae9130a7ae352443371cab90adc8817ee208c)) * autobump bio/gatk3/printreads ([#2683](https://www.github.com/snakemake/snakemake-wrappers/issues/2683)) ([c15b388](https://www.github.com/snakemake/snakemake-wrappers/commit/c15b3882c12d94a9b5a755dd851e94bbc65eca8f)) * autobump bio/gatk3/realignertargetcreator ([#2671](https://www.github.com/snakemake/snakemake-wrappers/issues/2671)) ([103425a](https://www.github.com/snakemake/snakemake-wrappers/commit/103425a18f9d4f194aa1794803faf5796e95fa54)) * autobump bio/igv-reports ([#2641](https://www.github.com/snakemake/snakemake-wrappers/issues/2641)) ([4bac92e](https://www.github.com/snakemake/snakemake-wrappers/commit/4bac92e374d7a5f977a67cfab0c92f1372e47be1)) * autobump bio/infernal/cmpress ([#2676](https://www.github.com/snakemake/snakemake-wrappers/issues/2676)) ([7e690c7](https://www.github.com/snakemake/snakemake-wrappers/commit/7e690c742c330d8ff195e920f9caf1643bbe1740)) * autobump bio/infernal/cmscan ([#2675](https://www.github.com/snakemake/snakemake-wrappers/issues/2675)) ([89eac39](https://www.github.com/snakemake/snakemake-wrappers/commit/89eac394bf1c2c183f21e734180398cc902b2455)) * autobump bio/jellyfish/count ([#2643](https://www.github.com/snakemake/snakemake-wrappers/issues/2643)) ([68d8bd6](https://www.github.com/snakemake/snakemake-wrappers/commit/68d8bd6d4c2900a872345a99bbb7c27fc3947fee)) * autobump bio/jellyfish/dump ([#2645](https://www.github.com/snakemake/snakemake-wrappers/issues/2645)) ([d3823f8](https://www.github.com/snakemake/snakemake-wrappers/commit/d3823f8b76565881aa3c451d9a781137538196e3)) * autobump bio/jellyfish/histo ([#2642](https://www.github.com/snakemake/snakemake-wrappers/issues/2642)) ([26c3123](https://www.github.com/snakemake/snakemake-wrappers/commit/26c3123627886f23160c55ac2555b186032cd2cf)) * autobump bio/jellyfish/merge ([#2644](https://www.github.com/snakemake/snakemake-wrappers/issues/2644)) ([2acb46b](https://www.github.com/snakemake/snakemake-wrappers/commit/2acb46b008bd2feaebda5c7d3952cf80e66fbc87)) * autobump bio/last/lastal ([#2632](https://www.github.com/snakemake/snakemake-wrappers/issues/2632)) ([0090d1a](https://www.github.com/snakemake/snakemake-wrappers/commit/0090d1a294c8b56738a9377ce420ebea27fab10c)) * autobump bio/last/lastal ([#2646](https://www.github.com/snakemake/snakemake-wrappers/issues/2646)) ([aecf702](https://www.github.com/snakemake/snakemake-wrappers/commit/aecf702f448f8bf449263d20d91518066af7ac69)) * autobump bio/last/lastal ([#2687](https://www.github.com/snakemake/snakemake-wrappers/issues/2687)) ([c252386](https://www.github.com/snakemake/snakemake-wrappers/commit/c25238635182b24f6e4c7fa09e0d8543fa5cb703)) * autobump bio/last/lastdb ([#2633](https://www.github.com/snakemake/snakemake-wrappers/issues/2633)) ([0adfac7](https://www.github.com/snakemake/snakemake-wrappers/commit/0adfac781ccf609b15bb4301a8597d52504d5049)) * autobump bio/last/lastdb ([#2647](https://www.github.com/snakemake/snakemake-wrappers/issues/2647)) ([9797636](https://www.github.com/snakemake/snakemake-wrappers/commit/979763663965ff14a19b8ae41dd744d6687c0dab)) * autobump bio/last/lastdb ([#2688](https://www.github.com/snakemake/snakemake-wrappers/issues/2688)) ([3dec479](https://www.github.com/snakemake/snakemake-wrappers/commit/3dec47921eee6532b0c94ba976c078dd61aae48d)) * autobump bio/multiqc ([#2677](https://www.github.com/snakemake/snakemake-wrappers/issues/2677)) ([197ef10](https://www.github.com/snakemake/snakemake-wrappers/commit/197ef1075a0c3676a0f3482c2b056e35cc8b7faa)) * autobump bio/seqkit ([#2635](https://www.github.com/snakemake/snakemake-wrappers/issues/2635)) ([8ed8105](https://www.github.com/snakemake/snakemake-wrappers/commit/8ed810512db5c7c76348993317320755d500ebe9)) * autobump bio/sourmash/compute ([#2678](https://www.github.com/snakemake/snakemake-wrappers/issues/2678)) ([1ba1a52](https://www.github.com/snakemake/snakemake-wrappers/commit/1ba1a52ebe2a3041178ba5ee93d6b1e0c8ce3d0c)) * autobump bio/spades/metaspades ([#2689](https://www.github.com/snakemake/snakemake-wrappers/issues/2689)) ([35e4c20](https://www.github.com/snakemake/snakemake-wrappers/commit/35e4c20760c9ae51fb46c2041178794d78965fe5)) * autobump bio/star/align ([#2634](https://www.github.com/snakemake/snakemake-wrappers/issues/2634)) ([0cb085a](https://www.github.com/snakemake/snakemake-wrappers/commit/0cb085a0fa6fd8466f0305350190464c8256850d)) * autobump bio/star/index ([#2636](https://www.github.com/snakemake/snakemake-wrappers/issues/2636)) ([e8df2fe](https://www.github.com/snakemake/snakemake-wrappers/commit/e8df2fe9cab9dc52575f771f170f0bdc0827aae0)) * autobump bio/ucsc/gtfToGenePred ([#2679](https://www.github.com/snakemake/snakemake-wrappers/issues/2679)) ([20682f2](https://www.github.com/snakemake/snakemake-wrappers/commit/20682f297038923eda28d5fb08388dbb555298ec)) * autobump bio/vep/cache ([#2690](https://www.github.com/snakemake/snakemake-wrappers/issues/2690)) ([0ea80f3](https://www.github.com/snakemake/snakemake-wrappers/commit/0ea80f342544af0552d99f6eb184eaab4314bc35)) * autobump bio/vep/plugins ([#2691](https://www.github.com/snakemake/snakemake-wrappers/issues/2691)) ([1b0108f](https://www.github.com/snakemake/snakemake-wrappers/commit/1b0108f96b23f50dae124c03b4b6b18e69163a4f)) * autobump bio/whatshap/haplotag ([#2637](https://www.github.com/snakemake/snakemake-wrappers/issues/2637)) ([5705ffc](https://www.github.com/snakemake/snakemake-wrappers/commit/5705ffc957a8d307c42920608d2a0f1e388a24ce)) * Update datavzrd to v2.36.1 ([#2692](https://www.github.com/snakemake/snakemake-wrappers/issues/2692)) ([cba4946](https://www.github.com/snakemake/snakemake-wrappers/commit/cba4946c8bef80ed3633f5b4a67a46ecee21a389)) --- 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>
votti
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Jun 22, 2024
<!-- 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--> According to the manual, `-m` specifies the approximated maximum required memory per thread. In some cases, `samtools sort` can use more memory than specified (e.g. samtools/samtools#831) so we account for some overhead. ### 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), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * 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).
votti
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Jun 22, 2024
🤖 I have created a release \*beep\* \*boop\* --- ### [3.3.7](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.3.6...v3.3.7) (2024-02-27) ### Bug Fixes * account for memory overhead ([snakemake#2648](https://www.github.com/snakemake/snakemake-wrappers/issues/2648)) ([6a05aad](https://www.github.com/snakemake/snakemake-wrappers/commit/6a05aad6066b0f3aadb92e1f7f931c161222b150)) ### Performance Improvements * autobump bio/bbtools ([snakemake#2627](https://www.github.com/snakemake/snakemake-wrappers/issues/2627)) ([7f5b520](https://www.github.com/snakemake/snakemake-wrappers/commit/7f5b5209923401ec20fd1a08063821767300b40a)) * autobump bio/diamond/blastp ([snakemake#2630](https://www.github.com/snakemake/snakemake-wrappers/issues/2630)) ([3911776](https://www.github.com/snakemake/snakemake-wrappers/commit/39117768d8978f51fade713abf843d970f98c623)) * autobump bio/diamond/blastx ([snakemake#2629](https://www.github.com/snakemake/snakemake-wrappers/issues/2629)) ([faf5de8](https://www.github.com/snakemake/snakemake-wrappers/commit/faf5de8da5579e97620f668b6f6ac63dc57cc0b4)) * autobump bio/diamond/makedb ([snakemake#2628](https://www.github.com/snakemake/snakemake-wrappers/issues/2628)) ([7ddca67](https://www.github.com/snakemake/snakemake-wrappers/commit/7ddca679c07cc79598f4099ba0f17d3f10a4247f)) * autobump bio/encode_fastq_downloader ([snakemake#2682](https://www.github.com/snakemake/snakemake-wrappers/issues/2682)) ([eb4a093](https://www.github.com/snakemake/snakemake-wrappers/commit/eb4a0939a1c6de100d1c1689d8cbb32402c8d328)) * autobump bio/fgbio/collectduplexseqmetrics ([snakemake#2631](https://www.github.com/snakemake/snakemake-wrappers/issues/2631)) ([7a58ee9](https://www.github.com/snakemake/snakemake-wrappers/commit/7a58ee99d23d1f75024bf2e12cb82c3e99bdeefc)) * autobump bio/galah ([snakemake#2670](https://www.github.com/snakemake/snakemake-wrappers/issues/2670)) ([8972be1](https://www.github.com/snakemake/snakemake-wrappers/commit/8972be1d8625cd2a359088fb41bdec0945030a9e)) * autobump bio/gatk/applybqsr ([snakemake#2662](https://www.github.com/snakemake/snakemake-wrappers/issues/2662)) ([2d1ff8e](https://www.github.com/snakemake/snakemake-wrappers/commit/2d1ff8eeb36fd82f33e03149f2205cc795993f85)) * autobump bio/gatk/applybqsrspark ([snakemake#2669](https://www.github.com/snakemake/snakemake-wrappers/issues/2669)) ([46a8acd](https://www.github.com/snakemake/snakemake-wrappers/commit/46a8acdff97cef5ff1e064ccedac90ba05659bb6)) * autobump bio/gatk/baserecalibratorspark ([snakemake#2651](https://www.github.com/snakemake/snakemake-wrappers/issues/2651)) ([3b4f517](https://www.github.com/snakemake/snakemake-wrappers/commit/3b4f51740d2a5b371789385fbd0ffe307af100f5)) * autobump bio/gatk/calculatecontamination ([snakemake#2673](https://www.github.com/snakemake/snakemake-wrappers/issues/2673)) ([056c9a0](https://www.github.com/snakemake/snakemake-wrappers/commit/056c9a0cb2f9198a700c1972d0ab7879a7178cdf)) * autobump bio/gatk/callcopyratiosegments ([snakemake#2655](https://www.github.com/snakemake/snakemake-wrappers/issues/2655)) ([b1932ae](https://www.github.com/snakemake/snakemake-wrappers/commit/b1932ae110fd9e52b7a4c782ed72c98636a84fc0)) * autobump bio/gatk/cleansam ([snakemake#2660](https://www.github.com/snakemake/snakemake-wrappers/issues/2660)) ([3802099](https://www.github.com/snakemake/snakemake-wrappers/commit/3802099d38708052cef5284bb3ec93d64e362f58)) * autobump bio/gatk/collectreadcounts ([snakemake#2666](https://www.github.com/snakemake/snakemake-wrappers/issues/2666)) ([0aa2cce](https://www.github.com/snakemake/snakemake-wrappers/commit/0aa2ccee2a6b763dc4fe83da11ed9827276b34a5)) * autobump bio/gatk/combinegvcfs ([snakemake#2686](https://www.github.com/snakemake/snakemake-wrappers/issues/2686)) ([a903745](https://www.github.com/snakemake/snakemake-wrappers/commit/a903745748b38685cfa5c6381abdcfbfce80803e)) * autobump bio/gatk/denoisereadcounts ([snakemake#2685](https://www.github.com/snakemake/snakemake-wrappers/issues/2685)) ([1e8498b](https://www.github.com/snakemake/snakemake-wrappers/commit/1e8498b5c7771ea2f7c360abeb640e6caa665db4)) * autobump bio/gatk/depthofcoverage ([snakemake#2658](https://www.github.com/snakemake/snakemake-wrappers/issues/2658)) ([1f43492](https://www.github.com/snakemake/snakemake-wrappers/commit/1f434923e7d4c0cc2905b3f6f17e1735577e8631)) * autobump bio/gatk/estimatelibrarycomplexity ([snakemake#2650](https://www.github.com/snakemake/snakemake-wrappers/issues/2650)) ([e9395ff](https://www.github.com/snakemake/snakemake-wrappers/commit/e9395ff31acaa58506258905f62582f9db0a55c0)) * autobump bio/gatk/filtermutectcalls ([snakemake#2684](https://www.github.com/snakemake/snakemake-wrappers/issues/2684)) ([b239e62](https://www.github.com/snakemake/snakemake-wrappers/commit/b239e62c5d0d67b138d9af77d8318db9e62dd9af)) * autobump bio/gatk/genomicsdbimport ([snakemake#2665](https://www.github.com/snakemake/snakemake-wrappers/issues/2665)) ([a38b278](https://www.github.com/snakemake/snakemake-wrappers/commit/a38b278adbb28857b59d25c0acca53daf6e2478f)) * autobump bio/gatk/getpileupsummaries ([snakemake#2657](https://www.github.com/snakemake/snakemake-wrappers/issues/2657)) ([7523193](https://www.github.com/snakemake/snakemake-wrappers/commit/75231932739bd97c39814a4b819c119288b6bddb)) * autobump bio/gatk/learnreadorientationmodel ([snakemake#2653](https://www.github.com/snakemake/snakemake-wrappers/issues/2653)) ([773e78c](https://www.github.com/snakemake/snakemake-wrappers/commit/773e78c49e9c4f70291f2a98d99852fe347bc244)) * autobump bio/gatk/leftalignandtrimvariants ([snakemake#2656](https://www.github.com/snakemake/snakemake-wrappers/issues/2656)) ([183950c](https://www.github.com/snakemake/snakemake-wrappers/commit/183950c6424d223915bca50deba31d5c3423d385)) * autobump bio/gatk/markduplicatesspark ([snakemake#2659](https://www.github.com/snakemake/snakemake-wrappers/issues/2659)) ([706cda3](https://www.github.com/snakemake/snakemake-wrappers/commit/706cda3432a12b4a7379edc4f146b2d29919535a)) * autobump bio/gatk/modelsegments ([snakemake#2663](https://www.github.com/snakemake/snakemake-wrappers/issues/2663)) ([bc40698](https://www.github.com/snakemake/snakemake-wrappers/commit/bc40698b6a902012a6a1e197eccfd58ec40d7910)) * autobump bio/gatk/mutect ([snakemake#2661](https://www.github.com/snakemake/snakemake-wrappers/issues/2661)) ([0e1d98a](https://www.github.com/snakemake/snakemake-wrappers/commit/0e1d98a96fe448279f38e31b871acf2abf5ca47e)) * autobump bio/gatk/scatterintervalsbyns ([snakemake#2674](https://www.github.com/snakemake/snakemake-wrappers/issues/2674)) ([e49b027](https://www.github.com/snakemake/snakemake-wrappers/commit/e49b0273bce205a3597ac2709e599c1ce1f18317)) * autobump bio/gatk/splitintervals ([snakemake#2667](https://www.github.com/snakemake/snakemake-wrappers/issues/2667)) ([332eed5](https://www.github.com/snakemake/snakemake-wrappers/commit/332eed549c82ef34d150da68e6af5dfd534ae467)) * autobump bio/gatk/splitncigarreads ([snakemake#2672](https://www.github.com/snakemake/snakemake-wrappers/issues/2672)) ([dabbc1e](https://www.github.com/snakemake/snakemake-wrappers/commit/dabbc1eec0f5805664a83d08f603a0dcd91407da)) * autobump bio/gatk/variantannotator ([snakemake#2664](https://www.github.com/snakemake/snakemake-wrappers/issues/2664)) ([2142589](https://www.github.com/snakemake/snakemake-wrappers/commit/21425891baf75967a8d6c1bb373168ce4e4bec4d)) * autobump bio/gatk/varianteval ([snakemake#2654](https://www.github.com/snakemake/snakemake-wrappers/issues/2654)) ([9d4ffea](https://www.github.com/snakemake/snakemake-wrappers/commit/9d4ffea301af15a5829d4f04b649431139475bc8)) * autobump bio/gatk/variantfiltration ([snakemake#2668](https://www.github.com/snakemake/snakemake-wrappers/issues/2668)) ([5cf5407](https://www.github.com/snakemake/snakemake-wrappers/commit/5cf54078192852b3de6f853c0a5fff0176dfbae0)) * autobump bio/gatk/variantrecalibrator ([snakemake#2652](https://www.github.com/snakemake/snakemake-wrappers/issues/2652)) ([714ae91](https://www.github.com/snakemake/snakemake-wrappers/commit/714ae9130a7ae352443371cab90adc8817ee208c)) * autobump bio/gatk3/printreads ([snakemake#2683](https://www.github.com/snakemake/snakemake-wrappers/issues/2683)) ([c15b388](https://www.github.com/snakemake/snakemake-wrappers/commit/c15b3882c12d94a9b5a755dd851e94bbc65eca8f)) * autobump bio/gatk3/realignertargetcreator ([snakemake#2671](https://www.github.com/snakemake/snakemake-wrappers/issues/2671)) ([103425a](https://www.github.com/snakemake/snakemake-wrappers/commit/103425a18f9d4f194aa1794803faf5796e95fa54)) * autobump bio/igv-reports ([snakemake#2641](https://www.github.com/snakemake/snakemake-wrappers/issues/2641)) ([4bac92e](https://www.github.com/snakemake/snakemake-wrappers/commit/4bac92e374d7a5f977a67cfab0c92f1372e47be1)) * autobump bio/infernal/cmpress ([snakemake#2676](https://www.github.com/snakemake/snakemake-wrappers/issues/2676)) ([7e690c7](https://www.github.com/snakemake/snakemake-wrappers/commit/7e690c742c330d8ff195e920f9caf1643bbe1740)) * autobump bio/infernal/cmscan ([snakemake#2675](https://www.github.com/snakemake/snakemake-wrappers/issues/2675)) ([89eac39](https://www.github.com/snakemake/snakemake-wrappers/commit/89eac394bf1c2c183f21e734180398cc902b2455)) * autobump bio/jellyfish/count ([snakemake#2643](https://www.github.com/snakemake/snakemake-wrappers/issues/2643)) ([68d8bd6](https://www.github.com/snakemake/snakemake-wrappers/commit/68d8bd6d4c2900a872345a99bbb7c27fc3947fee)) * autobump bio/jellyfish/dump ([snakemake#2645](https://www.github.com/snakemake/snakemake-wrappers/issues/2645)) ([d3823f8](https://www.github.com/snakemake/snakemake-wrappers/commit/d3823f8b76565881aa3c451d9a781137538196e3)) * autobump bio/jellyfish/histo ([snakemake#2642](https://www.github.com/snakemake/snakemake-wrappers/issues/2642)) ([26c3123](https://www.github.com/snakemake/snakemake-wrappers/commit/26c3123627886f23160c55ac2555b186032cd2cf)) * autobump bio/jellyfish/merge ([snakemake#2644](https://www.github.com/snakemake/snakemake-wrappers/issues/2644)) ([2acb46b](https://www.github.com/snakemake/snakemake-wrappers/commit/2acb46b008bd2feaebda5c7d3952cf80e66fbc87)) * autobump bio/last/lastal ([snakemake#2632](https://www.github.com/snakemake/snakemake-wrappers/issues/2632)) ([0090d1a](https://www.github.com/snakemake/snakemake-wrappers/commit/0090d1a294c8b56738a9377ce420ebea27fab10c)) * autobump bio/last/lastal ([snakemake#2646](https://www.github.com/snakemake/snakemake-wrappers/issues/2646)) ([aecf702](https://www.github.com/snakemake/snakemake-wrappers/commit/aecf702f448f8bf449263d20d91518066af7ac69)) * autobump bio/last/lastal ([snakemake#2687](https://www.github.com/snakemake/snakemake-wrappers/issues/2687)) ([c252386](https://www.github.com/snakemake/snakemake-wrappers/commit/c25238635182b24f6e4c7fa09e0d8543fa5cb703)) * autobump bio/last/lastdb ([snakemake#2633](https://www.github.com/snakemake/snakemake-wrappers/issues/2633)) ([0adfac7](https://www.github.com/snakemake/snakemake-wrappers/commit/0adfac781ccf609b15bb4301a8597d52504d5049)) * autobump bio/last/lastdb ([snakemake#2647](https://www.github.com/snakemake/snakemake-wrappers/issues/2647)) ([9797636](https://www.github.com/snakemake/snakemake-wrappers/commit/979763663965ff14a19b8ae41dd744d6687c0dab)) * autobump bio/last/lastdb ([snakemake#2688](https://www.github.com/snakemake/snakemake-wrappers/issues/2688)) ([3dec479](https://www.github.com/snakemake/snakemake-wrappers/commit/3dec47921eee6532b0c94ba976c078dd61aae48d)) * autobump bio/multiqc ([snakemake#2677](https://www.github.com/snakemake/snakemake-wrappers/issues/2677)) ([197ef10](https://www.github.com/snakemake/snakemake-wrappers/commit/197ef1075a0c3676a0f3482c2b056e35cc8b7faa)) * autobump bio/seqkit ([snakemake#2635](https://www.github.com/snakemake/snakemake-wrappers/issues/2635)) ([8ed8105](https://www.github.com/snakemake/snakemake-wrappers/commit/8ed810512db5c7c76348993317320755d500ebe9)) * autobump bio/sourmash/compute ([snakemake#2678](https://www.github.com/snakemake/snakemake-wrappers/issues/2678)) ([1ba1a52](https://www.github.com/snakemake/snakemake-wrappers/commit/1ba1a52ebe2a3041178ba5ee93d6b1e0c8ce3d0c)) * autobump bio/spades/metaspades ([snakemake#2689](https://www.github.com/snakemake/snakemake-wrappers/issues/2689)) ([35e4c20](https://www.github.com/snakemake/snakemake-wrappers/commit/35e4c20760c9ae51fb46c2041178794d78965fe5)) * autobump bio/star/align ([snakemake#2634](https://www.github.com/snakemake/snakemake-wrappers/issues/2634)) ([0cb085a](https://www.github.com/snakemake/snakemake-wrappers/commit/0cb085a0fa6fd8466f0305350190464c8256850d)) * autobump bio/star/index ([snakemake#2636](https://www.github.com/snakemake/snakemake-wrappers/issues/2636)) ([e8df2fe](https://www.github.com/snakemake/snakemake-wrappers/commit/e8df2fe9cab9dc52575f771f170f0bdc0827aae0)) * autobump bio/ucsc/gtfToGenePred ([snakemake#2679](https://www.github.com/snakemake/snakemake-wrappers/issues/2679)) ([20682f2](https://www.github.com/snakemake/snakemake-wrappers/commit/20682f297038923eda28d5fb08388dbb555298ec)) * autobump bio/vep/cache ([snakemake#2690](https://www.github.com/snakemake/snakemake-wrappers/issues/2690)) ([0ea80f3](https://www.github.com/snakemake/snakemake-wrappers/commit/0ea80f342544af0552d99f6eb184eaab4314bc35)) * autobump bio/vep/plugins ([snakemake#2691](https://www.github.com/snakemake/snakemake-wrappers/issues/2691)) ([1b0108f](https://www.github.com/snakemake/snakemake-wrappers/commit/1b0108f96b23f50dae124c03b4b6b18e69163a4f)) * autobump bio/whatshap/haplotag ([snakemake#2637](https://www.github.com/snakemake/snakemake-wrappers/issues/2637)) ([5705ffc](https://www.github.com/snakemake/snakemake-wrappers/commit/5705ffc957a8d307c42920608d2a0f1e388a24ce)) * Update datavzrd to v2.36.1 ([snakemake#2692](https://www.github.com/snakemake/snakemake-wrappers/issues/2692)) ([cba4946](https://www.github.com/snakemake/snakemake-wrappers/commit/cba4946c8bef80ed3633f5b4a67a46ecee21a389)) --- 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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According to the manual,
-m
specifies the approximated maximum required memory per thread.In some cases,
samtools sort
can use more memory than specified (e.g. samtools/samtools#831) so we account for some overhead.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,environment.yaml
pinning has been updated by runningsnakedeploy pin-conda-envs environment.yaml
on a linux machine,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,