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fix: gffread - properly generate fasta output #1797

Merged

fgvieira merged 1 commit into snakemake:master from isaacvock:fix-gffread

Sep 11, 2023

Contributor

isaacvock commented Sep 11, 2023

Description

Addresses bug discussed in detail in #1794. Details about proposed fix implemented in this PR are discussed in that issue report as well.


          Proper generation of fasta file output

f62c826

fgvieira approved these changes

View reviewed changes

fgvieira merged commit 89ea854 into snakemake:master

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johanneskoester pushed a commit that referenced this pull request


          chore: release 2.6.1 (#1782)

🤖 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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