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fix: genomepy wrapper #1795
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fix: genomepy wrapper #1795
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Since there is a default, you could also (line 42/43): |
@fgvieira you mean like this? Thanks for the feedback 馃槃 |
fgvieira
reviewed
Sep 12, 2023
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
fgvieira
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Sep 12, 2023
johanneskoester
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Oct 4, 2023
馃 I have created a release \*beep\* \*boop\* --- ### [2.6.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.6.0...v2.6.1) (2023-10-04) ### Bug Fixes * build docs on fork ([#1800](https://www.github.com/snakemake/snakemake-wrappers/issues/1800)) ([d859765](https://www.github.com/snakemake/snakemake-wrappers/commit/d85976505651052a00777fddcc0bf2178fbf0e4a)) * fix freebayes parallel ([#1807](https://www.github.com/snakemake/snakemake-wrappers/issues/1807)) ([2aa2f62](https://www.github.com/snakemake/snakemake-wrappers/commit/2aa2f62af06213d3060378b5600c10d5e79787fa)) * Fix MultiQC output file issues ([#1796](https://www.github.com/snakemake/snakemake-wrappers/issues/1796)) ([ecc45e8](https://www.github.com/snakemake/snakemake-wrappers/commit/ecc45e819f5e72b71ee777fa336da8c61a84758c)) * genomepy wrapper ([#1795](https://www.github.com/snakemake/snakemake-wrappers/issues/1795)) ([53231a0](https://www.github.com/snakemake/snakemake-wrappers/commit/53231a0ef6b9e8045081456e2a129fccfb744f18)) * gffread - properly generate fasta output ([#1797](https://www.github.com/snakemake/snakemake-wrappers/issues/1797)) ([89ea854](https://www.github.com/snakemake/snakemake-wrappers/commit/89ea854d1f2e26bed121650e3ae9f60a1ab84dec)) ### Performance Improvements * autobump bio/blast/makeblastdb ([#1786](https://www.github.com/snakemake/snakemake-wrappers/issues/1786)) ([a5db830](https://www.github.com/snakemake/snakemake-wrappers/commit/a5db830243346385601ab9c0851f221276df3342)) * autobump bio/bwa-mem2/mem ([#1826](https://www.github.com/snakemake/snakemake-wrappers/issues/1826)) ([37665c1](https://www.github.com/snakemake/snakemake-wrappers/commit/37665c12b4ba2760f0e078e781717ac9fa4efad8)) * autobump bio/bwa-memx/mem ([#1802](https://www.github.com/snakemake/snakemake-wrappers/issues/1802)) ([9ceb997](https://www.github.com/snakemake/snakemake-wrappers/commit/9ceb9974e99677accdfdbca32e17c496f880a901)) * autobump bio/bwa/samse ([#1831](https://www.github.com/snakemake/snakemake-wrappers/issues/1831)) ([8f93262](https://www.github.com/snakemake/snakemake-wrappers/commit/8f932627d344ded2331b396d6e585170bfaa4010)) * autobump bio/bwa/samxe ([#1833](https://www.github.com/snakemake/snakemake-wrappers/issues/1833)) ([95799fc](https://www.github.com/snakemake/snakemake-wrappers/commit/95799fc241a2cfb541464cba62f63056b350a0b7)) * autobump bio/deeptools/alignmentsieve ([#1790](https://www.github.com/snakemake/snakemake-wrappers/issues/1790)) ([cfa4cf7](https://www.github.com/snakemake/snakemake-wrappers/commit/cfa4cf7ca443a0d24858c804a55e563827e550b3)) * autobump bio/deeptools/alignmentsieve ([#1832](https://www.github.com/snakemake/snakemake-wrappers/issues/1832)) ([2623b3a](https://www.github.com/snakemake/snakemake-wrappers/commit/2623b3afce1baada662237259f4c3d6c2b3a5d33)) * autobump bio/deeptools/computematrix ([#1784](https://www.github.com/snakemake/snakemake-wrappers/issues/1784)) ([ccb2958](https://www.github.com/snakemake/snakemake-wrappers/commit/ccb2958e27d0ce3d5db13bbcf17581b3a6ccc0ae)) * autobump bio/deeptools/plotcoverage ([#1815](https://www.github.com/snakemake/snakemake-wrappers/issues/1815)) ([693e904](https://www.github.com/snakemake/snakemake-wrappers/commit/693e90453a938806b7b395a9db6c0f773f50f866)) * autobump bio/deeptools/plotprofile ([#1830](https://www.github.com/snakemake/snakemake-wrappers/issues/1830)) ([6f49c46](https://www.github.com/snakemake/snakemake-wrappers/commit/6f49c466ae3737afec0d3b4632625a9d4d62967d)) * autobump bio/deseq2/wald ([#1804](https://www.github.com/snakemake/snakemake-wrappers/issues/1804)) ([fbc6345](https://www.github.com/snakemake/snakemake-wrappers/commit/fbc6345cdaee3c1452aba52dfa007603b90a5d4f)) * autobump bio/gatk/combinegvcfs ([#1817](https://www.github.com/snakemake/snakemake-wrappers/issues/1817)) ([1cc8adc](https://www.github.com/snakemake/snakemake-wrappers/commit/1cc8adc07817b40746ec8ec58146e4f301ecf258)) * autobump bio/gatk3/baserecalibrator ([#1792](https://www.github.com/snakemake/snakemake-wrappers/issues/1792)) ([7b1b2c3](https://www.github.com/snakemake/snakemake-wrappers/commit/7b1b2c3c7eb05867b5cc770a28f65323b2cc18c4)) * autobump bio/gatk3/indelrealigner ([#1835](https://www.github.com/snakemake/snakemake-wrappers/issues/1835)) ([3d3d31c](https://www.github.com/snakemake/snakemake-wrappers/commit/3d3d31c9df0c9af9e1311cb691b7061c2f5a3fa9)) * autobump bio/gatk3/printreads ([#1839](https://www.github.com/snakemake/snakemake-wrappers/issues/1839)) ([c1d182a](https://www.github.com/snakemake/snakemake-wrappers/commit/c1d182a1dbbe3a70c9b7db2fae50e73224cba021)) * autobump bio/gatk3/realignertargetcreator ([#1814](https://www.github.com/snakemake/snakemake-wrappers/issues/1814)) ([0936b25](https://www.github.com/snakemake/snakemake-wrappers/commit/0936b25c211323af2cac819fc4d7982aad3bfa2c)) * autobump bio/gdc-api/bam-slicing ([#1806](https://www.github.com/snakemake/snakemake-wrappers/issues/1806)) ([f723338](https://www.github.com/snakemake/snakemake-wrappers/commit/f72333859b9f536990c22899ae2a720010a91d5d)) * autobump bio/igv-reports ([#1788](https://www.github.com/snakemake/snakemake-wrappers/issues/1788)) ([3ecdb17](https://www.github.com/snakemake/snakemake-wrappers/commit/3ecdb179679859e5ad8561f93c7476ef9430525c)) * autobump bio/meryl/count ([#1787](https://www.github.com/snakemake/snakemake-wrappers/issues/1787)) ([486d99b](https://www.github.com/snakemake/snakemake-wrappers/commit/486d99ba318e6a7b806077003f97f7b693e98a1d)) * autobump bio/multiqc ([#1811](https://www.github.com/snakemake/snakemake-wrappers/issues/1811)) ([221db0b](https://www.github.com/snakemake/snakemake-wrappers/commit/221db0b94a6a4f3658ce6a258bd868dc39ac79bd)) * autobump bio/pbmm2/align ([#1783](https://www.github.com/snakemake/snakemake-wrappers/issues/1783)) ([756a11d](https://www.github.com/snakemake/snakemake-wrappers/commit/756a11d317cdd332771925ae910c25eef39ea83e)) * autobump bio/pbmm2/index ([#1801](https://www.github.com/snakemake/snakemake-wrappers/issues/1801)) ([a91b214](https://www.github.com/snakemake/snakemake-wrappers/commit/a91b214b643452561bd3de81a6283c100471a427)) * autobump bio/picard/collectalignmentsummarymetrics ([#1803](https://www.github.com/snakemake/snakemake-wrappers/issues/1803)) ([3d727b4](https://www.github.com/snakemake/snakemake-wrappers/commit/3d727b4559cb8c2eb2a98d714b6a5f54d336b9c4)) * autobump bio/picard/collectmultiplemetrics ([#1791](https://www.github.com/snakemake/snakemake-wrappers/issues/1791)) ([a289b27](https://www.github.com/snakemake/snakemake-wrappers/commit/a289b276540d2da42920db86f9117090c8f39ddc)) * autobump bio/picard/collecttargetedpcrmetrics ([#1810](https://www.github.com/snakemake/snakemake-wrappers/issues/1810)) ([c64d4fd](https://www.github.com/snakemake/snakemake-wrappers/commit/c64d4fdf2c3da9ad31b40317678da3bb9937cfef)) * autobump bio/picard/createsequencedictionary ([#1812](https://www.github.com/snakemake/snakemake-wrappers/issues/1812)) ([3477e80](https://www.github.com/snakemake/snakemake-wrappers/commit/3477e80abdfa47c61f6c59c12530270fc81fd6ae)) * autobump bio/picard/markduplicates ([#1837](https://www.github.com/snakemake/snakemake-wrappers/issues/1837)) ([4e6af3d](https://www.github.com/snakemake/snakemake-wrappers/commit/4e6af3d7ce8c5d72698233d0515286759df7e8e4)) * autobump bio/picard/mergesamfiles ([#1818](https://www.github.com/snakemake/snakemake-wrappers/issues/1818)) ([0768970](https://www.github.com/snakemake/snakemake-wrappers/commit/07689707f145ad856a38dd47854b029421adf35c)) * autobump bio/picard/revertsam ([#1825](https://www.github.com/snakemake/snakemake-wrappers/issues/1825)) ([042589a](https://www.github.com/snakemake/snakemake-wrappers/commit/042589af84f216d12ad33ab7219efa7551c463d0)) * autobump bio/picard/samtofastq ([#1824](https://www.github.com/snakemake/snakemake-wrappers/issues/1824)) ([7a30dd8](https://www.github.com/snakemake/snakemake-wrappers/commit/7a30dd8191e4d0fb01a67dff22244ca9e0064bf3)) * autobump bio/picard/sortsam ([#1819](https://www.github.com/snakemake/snakemake-wrappers/issues/1819)) ([a7e1233](https://www.github.com/snakemake/snakemake-wrappers/commit/a7e1233d34f17c6dce50bc49b1a9b29dee1a7c0c)) * autobump bio/samtools/idxstats ([#1780](https://www.github.com/snakemake/snakemake-wrappers/issues/1780)) ([01985b9](https://www.github.com/snakemake/snakemake-wrappers/commit/01985b97b60be1ce4ca35958a5c4851ef98602dc)) * autobump bio/samtools/merge ([#1838](https://www.github.com/snakemake/snakemake-wrappers/issues/1838)) ([8a3c3c9](https://www.github.com/snakemake/snakemake-wrappers/commit/8a3c3c9276f41e3f4fc9085aa20fb164b06576a8)) * autobump bio/seqkit ([#1805](https://www.github.com/snakemake/snakemake-wrappers/issues/1805)) ([923c7ba](https://www.github.com/snakemake/snakemake-wrappers/commit/923c7bab7eb6dc4c8fb5825776c73c543e7a7207)) * autobump bio/spades/metaspades ([#1820](https://www.github.com/snakemake/snakemake-wrappers/issues/1820)) ([755343f](https://www.github.com/snakemake/snakemake-wrappers/commit/755343f58a0ec67f3d346b00a7ec8482fd461fa0)) * autobump bio/sra-tools/fasterq-dump ([#1793](https://www.github.com/snakemake/snakemake-wrappers/issues/1793)) ([873937e](https://www.github.com/snakemake/snakemake-wrappers/commit/873937e25308ede4a55fbf13698cb5e410aa8ad5)) * autobump bio/sra-tools/fasterq-dump ([#1813](https://www.github.com/snakemake/snakemake-wrappers/issues/1813)) ([ffdb0a4](https://www.github.com/snakemake/snakemake-wrappers/commit/ffdb0a4e64c4e5fbd8169ed6968416f5100dc285)) * autobump bio/star/align ([#1829](https://www.github.com/snakemake/snakemake-wrappers/issues/1829)) ([524917b](https://www.github.com/snakemake/snakemake-wrappers/commit/524917b4b8e0b02257cc02da5f128f2ef30ddd33)) * autobump bio/star/index ([#1836](https://www.github.com/snakemake/snakemake-wrappers/issues/1836)) ([0530063](https://www.github.com/snakemake/snakemake-wrappers/commit/05300632895eb4b1250de91a51e2c42b6da62adc)) * autobump bio/varscan/mpileup2indel ([#1821](https://www.github.com/snakemake/snakemake-wrappers/issues/1821)) ([cb2adbe](https://www.github.com/snakemake/snakemake-wrappers/commit/cb2adbe5cf4e0c73bd99f7454cdb2f64e66e1299)) * autobump bio/varscan/mpileup2snp ([#1827](https://www.github.com/snakemake/snakemake-wrappers/issues/1827)) ([40545ad](https://www.github.com/snakemake/snakemake-wrappers/commit/40545ad04b7bc37f36d97f562f19028b9d7e71ee)) * autobump bio/varscan/somatic ([#1834](https://www.github.com/snakemake/snakemake-wrappers/issues/1834)) ([a830aa7](https://www.github.com/snakemake/snakemake-wrappers/commit/a830aa7344c7edc8333d256c3fbf1ce2fb717e2a)) * autobump bio/vg/construct ([#1779](https://www.github.com/snakemake/snakemake-wrappers/issues/1779)) ([0a9bf2d](https://www.github.com/snakemake/snakemake-wrappers/commit/0a9bf2da9b053473069ac119db2a574790aa1112)) * autobump bio/vg/ids ([#1781](https://www.github.com/snakemake/snakemake-wrappers/issues/1781)) ([eb1e70e](https://www.github.com/snakemake/snakemake-wrappers/commit/eb1e70e7a0ce12c31be75d3ab682c9458164b9cd)) * autobump bio/vg/kmers ([#1828](https://www.github.com/snakemake/snakemake-wrappers/issues/1828)) ([5903848](https://www.github.com/snakemake/snakemake-wrappers/commit/5903848e1ac52f75c53fbd743f9847fe37a4be79)) * autobump bio/vg/merge ([#1816](https://www.github.com/snakemake/snakemake-wrappers/issues/1816)) ([6feb18f](https://www.github.com/snakemake/snakemake-wrappers/commit/6feb18fd1eb09b139c7c6018273afc9903d99fe2)) * autobump bio/vg/sim ([#1785](https://www.github.com/snakemake/snakemake-wrappers/issues/1785)) ([951ca2f](https://www.github.com/snakemake/snakemake-wrappers/commit/951ca2f81f2a03044af582fcc072f4dd7363c4a4)) --- 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
fixed the genomepy wrapper 馃コ
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,