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fix: Update environment.yaml of MultiQC #1873

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merged 3 commits into from Oct 18, 2023
Merged

fix: Update environment.yaml of MultiQC #1873

merged 3 commits into from Oct 18, 2023

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KuechlerO
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Description

Python version is fixed to versions<3.12.0 to handle dependency on imp-module, which is not available in newer python versions.
The imp module is deprecated in favor of importlib, and removed from the standard library since python version 3.12.0. Thus, depending on the python version your program-call/conda-environment is using, you will encounter a ModuleNotFoundError Error.

For further information, see discussion on StackOverflow: https://stackoverflow.com/questions/77273344/multiqc-snakemake-wrapper-modulenotfounderror-no-module-named-imp

@KuechlerO
Update environment.yaml
4f5eb35 
Python version is fixed to versions<3.12.0 to handle dependency on imp-module, which is not available in newer python versions. For further information, see discussion on StackOverflow: 
https://stackoverflow.com/questions/77273344/multiqc-snakemake-wrapper-modulenotfounderror-no-module-named-imp
@KuechlerO KuechlerO changed the title Bug Fixes: Update environment.yaml of MultiQC fix: Update environment.yaml of MultiQC Oct 13, 2023
@KuechlerO
Update environment.yaml
2892544 
Restrict python version to be >=3.7.0 (future feature annotation needs to be defined)
@fgvieira
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This issue is currently being fixed by MutiQC MultiQC/MultiQC#2112 and is expected to be fixed Monday, so it might be better to wait a bit.

@fgvieira fgvieira mentioned this pull request Oct 16, 2023
Closed
@fgvieira fgvieira enabled auto-merge (squash) October 18, 2023 07:02
@fgvieira fgvieira merged commit bcd4a24 into snakemake:master Oct 18, 2023
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@KuechlerO KuechlerO deleted the multiqc_wrapper_quick_fix branch October 18, 2023 14:21
johanneskoester pushed a commit that referenced this pull request Oct 23, 2023
@github-actions
chore: release 2.7.0 (#1876)
05d51db 
🤖 I have created a release \*beep\* \*boop\*
---
##
[2.7.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.6.1...v2.7.0)
(2023-10-23)


### Features

* Cnvkit call wrapper
([#1879](https://www.github.com/snakemake/snakemake-wrappers/issues/1879))
([db073db](https://www.github.com/snakemake/snakemake-wrappers/commit/db073dbfe00e19e71e198af2c809b8a71662a112))
* cnvkit diagram wrapper
([#1881](https://www.github.com/snakemake/snakemake-wrappers/issues/1881))
([d3cfc11](https://www.github.com/snakemake/snakemake-wrappers/commit/d3cfc1176e877f324a38c125aa6d3a6f4ad7f556))
* Cnvkit target wrapper
([#1878](https://www.github.com/snakemake/snakemake-wrappers/issues/1878))
([07f3b16](https://www.github.com/snakemake/snakemake-wrappers/commit/07f3b164d3f45512daff3c129bf5ce0e42608dae))
* whatshap haplotag
([#1862](https://www.github.com/snakemake/snakemake-wrappers/issues/1862))
([d55ed6a](https://www.github.com/snakemake/snakemake-wrappers/commit/d55ed6a5913bb79d89766c217e7f4700ebe6fe48))
* wrapper for cnvkit batch
([#1877](https://www.github.com/snakemake/snakemake-wrappers/issues/1877))
([40bfc5d](https://www.github.com/snakemake/snakemake-wrappers/commit/40bfc5d6b357b5be24fe4a51953dcaf7a44a7a1b))


### Bug Fixes

* Update environment.yaml of MultiQC
([#1873](https://www.github.com/snakemake/snakemake-wrappers/issues/1873))
([bcd4a24](https://www.github.com/snakemake/snakemake-wrappers/commit/bcd4a24f99bf6e289db22ffcadd670f91677d8d2))


### Performance Improvements

* autobump bio/bcftools/call
([#1855](https://www.github.com/snakemake/snakemake-wrappers/issues/1855))
([ef3ba47](https://www.github.com/snakemake/snakemake-wrappers/commit/ef3ba4738843404665dacd9a379c4b7dbe283119))
* autobump bio/bcftools/filter
([#1889](https://www.github.com/snakemake/snakemake-wrappers/issues/1889))
([088aa72](https://www.github.com/snakemake/snakemake-wrappers/commit/088aa721e040c7b6e27c156e610f10c645378d7d))
* autobump bio/bcftools/merge
([#1887](https://www.github.com/snakemake/snakemake-wrappers/issues/1887))
([43781d6](https://www.github.com/snakemake/snakemake-wrappers/commit/43781d6e7a2d2c356b216d8d9cb8474df829c085))
* autobump bio/bcftools/mpileup
([#1896](https://www.github.com/snakemake/snakemake-wrappers/issues/1896))
([0dcb3cc](https://www.github.com/snakemake/snakemake-wrappers/commit/0dcb3cc3a51eab6ce0996e0ec6e33949662dd251))
* autobump bio/bcftools/norm
([#1884](https://www.github.com/snakemake/snakemake-wrappers/issues/1884))
([30a9f95](https://www.github.com/snakemake/snakemake-wrappers/commit/30a9f95f98f18ff93b3411d374e08aa90cb15336))
* autobump bio/bcftools/reheader
([#1841](https://www.github.com/snakemake/snakemake-wrappers/issues/1841))
([f450530](https://www.github.com/snakemake/snakemake-wrappers/commit/f450530b5fe38fc8fd6d964b22fb535c99c91ae5))
* autobump bio/bcftools/stats
([#1883](https://www.github.com/snakemake/snakemake-wrappers/issues/1883))
([9ac746c](https://www.github.com/snakemake/snakemake-wrappers/commit/9ac746c3e73fcd4a484c16dda9a29ea945add33a))
* autobump bio/bcftools/view
([#1842](https://www.github.com/snakemake/snakemake-wrappers/issues/1842))
([19e89ab](https://www.github.com/snakemake/snakemake-wrappers/commit/19e89abed1d3daae3f5875650d899fd4abc0df17))
* autobump bio/bismark/bam2nuc
([#1867](https://www.github.com/snakemake/snakemake-wrappers/issues/1867))
([f29483a](https://www.github.com/snakemake/snakemake-wrappers/commit/f29483a63b6a81c99ec40ee3a250f221d2961a9d))
* autobump bio/bismark/bismark
([#1853](https://www.github.com/snakemake/snakemake-wrappers/issues/1853))
([6babc2a](https://www.github.com/snakemake/snakemake-wrappers/commit/6babc2a3881cccae83efc90b550bc4d96994fbab))
* autobump bio/bismark/bismark2bedGraph
([#1894](https://www.github.com/snakemake/snakemake-wrappers/issues/1894))
([6bd04db](https://www.github.com/snakemake/snakemake-wrappers/commit/6bd04dba4fbc94b1e671476c45c0668148551424))
* autobump bio/bismark/bismark2report
([#1871](https://www.github.com/snakemake/snakemake-wrappers/issues/1871))
([c5003d5](https://www.github.com/snakemake/snakemake-wrappers/commit/c5003d5c711c3fd48e49d73957d3494b8554339e))
* autobump bio/bismark/bismark2summary
([#1882](https://www.github.com/snakemake/snakemake-wrappers/issues/1882))
([3256aa1](https://www.github.com/snakemake/snakemake-wrappers/commit/3256aa1fe77ecf9773cc7531c9aca34aca142f17))
* autobump bio/bismark/deduplicate_bismark
([#1846](https://www.github.com/snakemake/snakemake-wrappers/issues/1846))
([b18c5c7](https://www.github.com/snakemake/snakemake-wrappers/commit/b18c5c76149a3d2065273bc7bbf7779719e15a1d))
* autobump bio/bowtie2/build
([#1893](https://www.github.com/snakemake/snakemake-wrappers/issues/1893))
([dc2f765](https://www.github.com/snakemake/snakemake-wrappers/commit/dc2f765252cac563fb16a84c3c4d6892ab0c5f9d))
* autobump bio/bwa-meme/mem
([#1861](https://www.github.com/snakemake/snakemake-wrappers/issues/1861))
([31be794](https://www.github.com/snakemake/snakemake-wrappers/commit/31be794f7961dbb2eb627e9726ce80377de5f981))
* autobump bio/bwa/samxe
([#1895](https://www.github.com/snakemake/snakemake-wrappers/issues/1895))
([929ddd6](https://www.github.com/snakemake/snakemake-wrappers/commit/929ddd60ac6c9ea77540b3d250a415221222555a))
* autobump bio/deeptools/computematrix
([#1848](https://www.github.com/snakemake/snakemake-wrappers/issues/1848))
([0fdcd5a](https://www.github.com/snakemake/snakemake-wrappers/commit/0fdcd5a0809b6843cac2a2fbd2fe2b85c6514e39))
* autobump bio/gatk/applybqsr
([#1866](https://www.github.com/snakemake/snakemake-wrappers/issues/1866))
([201dea6](https://www.github.com/snakemake/snakemake-wrappers/commit/201dea66f82fade2ece26538cbbf797277c974a7))
* autobump bio/gatk3/baserecalibrator
([#1847](https://www.github.com/snakemake/snakemake-wrappers/issues/1847))
([80edec6](https://www.github.com/snakemake/snakemake-wrappers/commit/80edec6b4ee9b378c124653727185774f32b11bc))
* autobump bio/gatk3/indelrealigner
([#1890](https://www.github.com/snakemake/snakemake-wrappers/issues/1890))
([7803fbe](https://www.github.com/snakemake/snakemake-wrappers/commit/7803fbebec46711a46e7748d2a51e161db0794e6))
* autobump bio/gatk3/printreads
([#1869](https://www.github.com/snakemake/snakemake-wrappers/issues/1869))
([58fe71a](https://www.github.com/snakemake/snakemake-wrappers/commit/58fe71ab5e022df46ed7bb157352b202166b1086))
* autobump bio/lofreq/call
([#1860](https://www.github.com/snakemake/snakemake-wrappers/issues/1860))
([ca5409d](https://www.github.com/snakemake/snakemake-wrappers/commit/ca5409d7b0e8d9abc82cc3fce57b8ae8b0f1d702))
* autobump bio/mashmap
([#1886](https://www.github.com/snakemake/snakemake-wrappers/issues/1886))
([4d277b2](https://www.github.com/snakemake/snakemake-wrappers/commit/4d277b2dcf33bb359244137e44d3da9b222f878b))
* autobump bio/paladin/align
([#1897](https://www.github.com/snakemake/snakemake-wrappers/issues/1897))
([7b5dc11](https://www.github.com/snakemake/snakemake-wrappers/commit/7b5dc11b916c734f484493459776555a0e561276))
* autobump bio/pandora/index
([#1868](https://www.github.com/snakemake/snakemake-wrappers/issues/1868))
([bc7b88a](https://www.github.com/snakemake/snakemake-wrappers/commit/bc7b88a970972a56e7ba64060294bdd1f853171b))
* autobump bio/picard/collecthsmetrics
([#1865](https://www.github.com/snakemake/snakemake-wrappers/issues/1865))
([6028b5d](https://www.github.com/snakemake/snakemake-wrappers/commit/6028b5d43a9422b3e9b23d950c9d574196e53c14))
* autobump bio/picard/collectrnaseqmetrics
([#1844](https://www.github.com/snakemake/snakemake-wrappers/issues/1844))
([bd4ac2f](https://www.github.com/snakemake/snakemake-wrappers/commit/bd4ac2f0c14136c4c4b9fe44bf9f9b6721cbc318))
* autobump bio/pretext/map
([#1851](https://www.github.com/snakemake/snakemake-wrappers/issues/1851))
([f4bb492](https://www.github.com/snakemake/snakemake-wrappers/commit/f4bb49242f87c5df15eb0d2071cbe3a8cb69f2be))
* autobump bio/salmon/quant
([#1888](https://www.github.com/snakemake/snakemake-wrappers/issues/1888))
([af65c24](https://www.github.com/snakemake/snakemake-wrappers/commit/af65c24c53bfd53ff73147273d662ab714d6418e))
* autobump bio/samtools/calmd
([#1843](https://www.github.com/snakemake/snakemake-wrappers/issues/1843))
([3c5bd68](https://www.github.com/snakemake/snakemake-wrappers/commit/3c5bd6885af82d589d64e863b45b2b8fc328f570))
* autobump bio/samtools/faidx
([#1891](https://www.github.com/snakemake/snakemake-wrappers/issues/1891))
([2d4444e](https://www.github.com/snakemake/snakemake-wrappers/commit/2d4444e3e98320dbe42a2312de2b7b34a57b3ab4))
* autobump bio/samtools/index
([#1849](https://www.github.com/snakemake/snakemake-wrappers/issues/1849))
([2dd024c](https://www.github.com/snakemake/snakemake-wrappers/commit/2dd024ca903d67ecb95b94821746ab5d90d0f1f3))
* autobump bio/snpeff/download
([#1892](https://www.github.com/snakemake/snakemake-wrappers/issues/1892))
([920eb68](https://www.github.com/snakemake/snakemake-wrappers/commit/920eb68334dc17b21e246b85646a60b8174ab5d4))
* autobump bio/snpsift/dbnsfp
([#1852](https://www.github.com/snakemake/snakemake-wrappers/issues/1852))
([f8453d6](https://www.github.com/snakemake/snakemake-wrappers/commit/f8453d6c40d7bb4c56f03b4fbbbadaf1b28a8097))
* autobump bio/snpsift/dbnsfp
([#1898](https://www.github.com/snakemake/snakemake-wrappers/issues/1898))
([3b48591](https://www.github.com/snakemake/snakemake-wrappers/commit/3b48591460656f3a4799b2ec3d31cf6d1746c29d))
* autobump bio/snpsift/gwascat
([#1870](https://www.github.com/snakemake/snakemake-wrappers/issues/1870))
([c55a0b5](https://www.github.com/snakemake/snakemake-wrappers/commit/c55a0b52ff99d6a093da64e6c2629042662452ec))
* autobump bio/snpsift/varType
([#1885](https://www.github.com/snakemake/snakemake-wrappers/issues/1885))
([b456dc5](https://www.github.com/snakemake/snakemake-wrappers/commit/b456dc55ca48d43c5d9187fa0243a03681d654db))
* autobump bio/spades/metaspades
([#1859](https://www.github.com/snakemake/snakemake-wrappers/issues/1859))
([ef24b5d](https://www.github.com/snakemake/snakemake-wrappers/commit/ef24b5da60de82893f461e9487cf2e477fb75228))
* autobump bio/tabix/query
([#1858](https://www.github.com/snakemake/snakemake-wrappers/issues/1858))
([59a11ca](https://www.github.com/snakemake/snakemake-wrappers/commit/59a11caf111a7b7740ec862219f9abad49945110))
* autobump bio/umis/bamtag
([#1872](https://www.github.com/snakemake/snakemake-wrappers/issues/1872))
([c44ef6b](https://www.github.com/snakemake/snakemake-wrappers/commit/c44ef6b6b7f54fe047e8a3c7c8c98b3a0327ebc4))
* autobump bio/vg/construct
([#1857](https://www.github.com/snakemake/snakemake-wrappers/issues/1857))
([addcbdc](https://www.github.com/snakemake/snakemake-wrappers/commit/addcbdc120b5980b2d85530ef99c4bfa0030e1b6))
* autobump bio/vg/ids
([#1854](https://www.github.com/snakemake/snakemake-wrappers/issues/1854))
([ea9934c](https://www.github.com/snakemake/snakemake-wrappers/commit/ea9934cfacbc7d9c8f1a97ff3e210e42d12bd931))
* autobump utils/datavzrd
([#1856](https://www.github.com/snakemake/snakemake-wrappers/issues/1856))
([723fd8b](https://www.github.com/snakemake/snakemake-wrappers/commit/723fd8b28eb139227e4fdbec18eaa7435cb11502))
---


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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@KuechlerO @fgvieira