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fix: bug when renaming samples #2293
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votti
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Nov 7, 2023
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Looks good to me - thanks a lot for promptly fixing this!
I first thought this would break backwards compatibility, but testing it it does not. Thanks again!
johanneskoester
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Nov 8, 2023
🤖 I have created a release \*beep\* \*boop\* --- ## [2.10.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.9.1...v2.10.0) (2023-11-08) ### Features * update datavzrd 2.29.0 ([#2288](https://www.github.com/snakemake/snakemake-wrappers/issues/2288)) ([02ca59a](https://www.github.com/snakemake/snakemake-wrappers/commit/02ca59af0b79d099c88bbd4407a3a7695e8a7848)) * update datavzrd 2.30.0 ([#2294](https://www.github.com/snakemake/snakemake-wrappers/issues/2294)) ([6c1750d](https://www.github.com/snakemake/snakemake-wrappers/commit/6c1750d9f915fc8c28a231ec575af7b9feafb65f)) ### Bug Fixes * bug when renaming samples ([#2293](https://www.github.com/snakemake/snakemake-wrappers/issues/2293)) ([8c217f8](https://www.github.com/snakemake/snakemake-wrappers/commit/8c217f8a86128deb7c5579ce35081e515434b6e9)) * fix datavzrd version pinning ([#2290](https://www.github.com/snakemake/snakemake-wrappers/issues/2290)) ([2f0cee7](https://www.github.com/snakemake/snakemake-wrappers/commit/2f0cee7fcaa3878e19534c05b2a4ac2c4d413c18)) ### Performance Improvements * autobump bio/bustools/sort ([#2234](https://www.github.com/snakemake/snakemake-wrappers/issues/2234)) ([3ce66d6](https://www.github.com/snakemake/snakemake-wrappers/commit/3ce66d627741904cb7903380900948f21d7902b6)) * autobump bio/bustools/text ([#2233](https://www.github.com/snakemake/snakemake-wrappers/issues/2233)) ([88185ac](https://www.github.com/snakemake/snakemake-wrappers/commit/88185acf6b74e1bc2280e54aaaab2a1e86ce2bed)) * autobump bio/deseq2/deseqdataset ([#2237](https://www.github.com/snakemake/snakemake-wrappers/issues/2237)) ([dfc5575](https://www.github.com/snakemake/snakemake-wrappers/commit/dfc5575b3364513c0530111043e2d961717b0c80)) * autobump bio/deseq2/wald ([#2236](https://www.github.com/snakemake/snakemake-wrappers/issues/2236)) ([8657895](https://www.github.com/snakemake/snakemake-wrappers/commit/8657895edeb9f2fc58a0837f5cccd94ef980d18f)) * autobump bio/fastp ([#2239](https://www.github.com/snakemake/snakemake-wrappers/issues/2239)) ([8b5947d](https://www.github.com/snakemake/snakemake-wrappers/commit/8b5947d8b6f24652eba036729d48a93957e6f08b)) * autobump bio/fastq_screen ([#2238](https://www.github.com/snakemake/snakemake-wrappers/issues/2238)) ([c75f5a2](https://www.github.com/snakemake/snakemake-wrappers/commit/c75f5a2faade1a5e6a89a9e05ab6688ce3a5951e)) * autobump bio/fastqc ([#2240](https://www.github.com/snakemake/snakemake-wrappers/issues/2240)) ([5b46013](https://www.github.com/snakemake/snakemake-wrappers/commit/5b46013824dda94c13e4a096e42eb34c4956f613)) * autobump bio/fgbio/annotatebamwithumis ([#2243](https://www.github.com/snakemake/snakemake-wrappers/issues/2243)) ([f7b8427](https://www.github.com/snakemake/snakemake-wrappers/commit/f7b842729e22695562df8601d172a02cd382ab00)) * autobump bio/fgbio/callmolecularconsensusreads ([#2244](https://www.github.com/snakemake/snakemake-wrappers/issues/2244)) ([0def80b](https://www.github.com/snakemake/snakemake-wrappers/commit/0def80b73c4f973d4c09de37ae3c5462e7e98209)) * autobump bio/fgbio/filterconsensusreads ([#2242](https://www.github.com/snakemake/snakemake-wrappers/issues/2242)) ([aed8b65](https://www.github.com/snakemake/snakemake-wrappers/commit/aed8b653dce7ea3f5813531ed8f88407309e4274)) * autobump bio/fgbio/groupreadsbyumi ([#2245](https://www.github.com/snakemake/snakemake-wrappers/issues/2245)) ([98ca646](https://www.github.com/snakemake/snakemake-wrappers/commit/98ca6462f82b24cfa9a1089b0f77f43454ccad68)) * autobump bio/filtlong ([#2241](https://www.github.com/snakemake/snakemake-wrappers/issues/2241)) ([2a5123f](https://www.github.com/snakemake/snakemake-wrappers/commit/2a5123f41cece081a3e03dd6c5a469552c8f585b)) * autobump bio/paladin/align ([#2270](https://www.github.com/snakemake/snakemake-wrappers/issues/2270)) ([e1d5293](https://www.github.com/snakemake/snakemake-wrappers/commit/e1d529342208c505a9aa25c09a288c9078ef9985)) * autobump bio/paladin/prepare ([#2277](https://www.github.com/snakemake/snakemake-wrappers/issues/2277)) ([5615116](https://www.github.com/snakemake/snakemake-wrappers/commit/5615116982038ef123b7eaeb63dd041a1df831bd)) * autobump bio/pbmm2/align ([#2269](https://www.github.com/snakemake/snakemake-wrappers/issues/2269)) ([6f2f6cf](https://www.github.com/snakemake/snakemake-wrappers/commit/6f2f6cf58aef9988fb2af0d2ee378a3c6c6d0234)) * autobump bio/pbmm2/index ([#2273](https://www.github.com/snakemake/snakemake-wrappers/issues/2273)) ([95eea96](https://www.github.com/snakemake/snakemake-wrappers/commit/95eea9646ddba88a5d38d945b75b6ef1d927e395)) * autobump bio/pear ([#2266](https://www.github.com/snakemake/snakemake-wrappers/issues/2266)) ([294be33](https://www.github.com/snakemake/snakemake-wrappers/commit/294be3391a8bb1704ebfab3e704df0749c4f286d)) * autobump bio/picard/addorreplacereadgroups ([#2259](https://www.github.com/snakemake/snakemake-wrappers/issues/2259)) ([bc422f3](https://www.github.com/snakemake/snakemake-wrappers/commit/bc422f3a7742faa648e421952d249e9452e1bed2)) * autobump bio/picard/bedtointervallist ([#2272](https://www.github.com/snakemake/snakemake-wrappers/issues/2272)) ([203b36a](https://www.github.com/snakemake/snakemake-wrappers/commit/203b36a4087ba4960f436d885961b71c6d4581d5)) * autobump bio/picard/collectalignmentsummarymetrics ([#2262](https://www.github.com/snakemake/snakemake-wrappers/issues/2262)) ([41e8dde](https://www.github.com/snakemake/snakemake-wrappers/commit/41e8dde0ecb9e4d7048cff9951d0806a31124c66)) * autobump bio/picard/collectgcbiasmetrics ([#2256](https://www.github.com/snakemake/snakemake-wrappers/issues/2256)) ([80b3cf6](https://www.github.com/snakemake/snakemake-wrappers/commit/80b3cf6b92cafc0e621a9829ff8ae9005d7f5d71)) * autobump bio/picard/collecthsmetrics ([#2257](https://www.github.com/snakemake/snakemake-wrappers/issues/2257)) ([ae663c2](https://www.github.com/snakemake/snakemake-wrappers/commit/ae663c2e72d5956625b8f107e78d3d3cc3ca0412)) * autobump bio/picard/collectinsertsizemetrics ([#2261](https://www.github.com/snakemake/snakemake-wrappers/issues/2261)) ([ef362b3](https://www.github.com/snakemake/snakemake-wrappers/commit/ef362b3cbcd7e8138c54e5ae57347d86bd1e1e6d)) * autobump bio/picard/collectmultiplemetrics ([#2248](https://www.github.com/snakemake/snakemake-wrappers/issues/2248)) ([f73efb6](https://www.github.com/snakemake/snakemake-wrappers/commit/f73efb6a6f30c51382a2837fb4d82769d2425286)) * autobump bio/picard/collectrnaseqmetrics ([#2250](https://www.github.com/snakemake/snakemake-wrappers/issues/2250)) ([c4f541b](https://www.github.com/snakemake/snakemake-wrappers/commit/c4f541b80a3a0cc2b85affc703aa02d6104f8add)) * autobump bio/picard/collecttargetedpcrmetrics ([#2263](https://www.github.com/snakemake/snakemake-wrappers/issues/2263)) ([2fb4af9](https://www.github.com/snakemake/snakemake-wrappers/commit/2fb4af954402e0ea66ae8b4494265c54f16fee21)) * autobump bio/picard/markduplicates ([#2276](https://www.github.com/snakemake/snakemake-wrappers/issues/2276)) ([93933d4](https://www.github.com/snakemake/snakemake-wrappers/commit/93933d408142d73093cdc87890faf1dc99de0452)) * autobump bio/picard/mergevcfs ([#2271](https://www.github.com/snakemake/snakemake-wrappers/issues/2271)) ([302d1ff](https://www.github.com/snakemake/snakemake-wrappers/commit/302d1ff942bdf57bb40fef322c018f1000b75585)) * autobump bio/picard/revertsam ([#2285](https://www.github.com/snakemake/snakemake-wrappers/issues/2285)) ([eee4daf](https://www.github.com/snakemake/snakemake-wrappers/commit/eee4daf752233ff0647b300fcb92499712ce0daf)) * autobump bio/picard/samtofastq ([#2280](https://www.github.com/snakemake/snakemake-wrappers/issues/2280)) ([803ddec](https://www.github.com/snakemake/snakemake-wrappers/commit/803ddec608bfd3414000f5285f6ebb9df588d3e8)) * autobump bio/picard/sortsam ([#2258](https://www.github.com/snakemake/snakemake-wrappers/issues/2258)) ([118b70d](https://www.github.com/snakemake/snakemake-wrappers/commit/118b70d5fa85cf257a2c29c71da4f9a0e4362fc9)) * autobump bio/pindel/call ([#2275](https://www.github.com/snakemake/snakemake-wrappers/issues/2275)) ([45c52d3](https://www.github.com/snakemake/snakemake-wrappers/commit/45c52d3b01b4e3f25d2682bfc2fdf67e8c7187df)) * autobump bio/pindel/pindel2vcf ([#2281](https://www.github.com/snakemake/snakemake-wrappers/issues/2281)) ([5ffe4bc](https://www.github.com/snakemake/snakemake-wrappers/commit/5ffe4bce3c7c7d07bce713b198f55402b2924bff)) * autobump bio/plass ([#2264](https://www.github.com/snakemake/snakemake-wrappers/issues/2264)) ([0d8ca7f](https://www.github.com/snakemake/snakemake-wrappers/commit/0d8ca7f058256c5e6aaba74030daa750639a056d)) * autobump bio/preseq/lc_extrap ([#2254](https://www.github.com/snakemake/snakemake-wrappers/issues/2254)) ([538e322](https://www.github.com/snakemake/snakemake-wrappers/commit/538e322bf3d3ad7f7c1a616d66b4b30c37113ead)) * autobump bio/pretext/graph ([#2251](https://www.github.com/snakemake/snakemake-wrappers/issues/2251)) ([f3c7296](https://www.github.com/snakemake/snakemake-wrappers/commit/f3c7296371f1dfd61753ea8b78f1d9c32413084f)) * autobump bio/pretext/map ([#2265](https://www.github.com/snakemake/snakemake-wrappers/issues/2265)) ([c6c35f8](https://www.github.com/snakemake/snakemake-wrappers/commit/c6c35f805cd933957f83700ac36540f15ca34a0a)) * autobump bio/pretext/snapshot ([#2282](https://www.github.com/snakemake/snakemake-wrappers/issues/2282)) ([a7358b9](https://www.github.com/snakemake/snakemake-wrappers/commit/a7358b9a2af8c34c9bd542b56aa4a49891d00ec2)) * autobump bio/prosolo/control-fdr ([#2268](https://www.github.com/snakemake/snakemake-wrappers/issues/2268)) ([c55a9ec](https://www.github.com/snakemake/snakemake-wrappers/commit/c55a9ecdbd2bfaa73525192ca8bd2ca8d62d6471)) * autobump bio/prosolo/single-cell-bulk ([#2253](https://www.github.com/snakemake/snakemake-wrappers/issues/2253)) ([03d4f9f](https://www.github.com/snakemake/snakemake-wrappers/commit/03d4f9f151edc5cdeee890510c37cd98bccc3b20)) * autobump bio/ptrimmer ([#2284](https://www.github.com/snakemake/snakemake-wrappers/issues/2284)) ([105ffd9](https://www.github.com/snakemake/snakemake-wrappers/commit/105ffd973ec63a61a6a78a185a899ee1d40cf682)) * autobump bio/purge_dups/calcuts ([#2249](https://www.github.com/snakemake/snakemake-wrappers/issues/2249)) ([72397c2](https://www.github.com/snakemake/snakemake-wrappers/commit/72397c20d4b8b1870c1588baf0aace517a03d1d6)) * autobump bio/purge_dups/get_seqs ([#2252](https://www.github.com/snakemake/snakemake-wrappers/issues/2252)) ([25a113c](https://www.github.com/snakemake/snakemake-wrappers/commit/25a113cec300a14f805b588ac27b19dd94c28c87)) * autobump bio/purge_dups/ngscstat ([#2267](https://www.github.com/snakemake/snakemake-wrappers/issues/2267)) ([f4e2068](https://www.github.com/snakemake/snakemake-wrappers/commit/f4e206860cec2518c14395278b509f6fab447b7b)) * autobump bio/purge_dups/pbcstat ([#2283](https://www.github.com/snakemake/snakemake-wrappers/issues/2283)) ([3893aa0](https://www.github.com/snakemake/snakemake-wrappers/commit/3893aa0a90fa15bbf3cfccf2b0cfcb8c8c6f0c8b)) * autobump bio/purge_dups/purge_dups ([#2278](https://www.github.com/snakemake/snakemake-wrappers/issues/2278)) ([a08e8f8](https://www.github.com/snakemake/snakemake-wrappers/commit/a08e8f83dbc62c06ceb5036c717f9d2b8e605f70)) * autobump bio/purge_dups/split_fa ([#2279](https://www.github.com/snakemake/snakemake-wrappers/issues/2279)) ([26dbb9e](https://www.github.com/snakemake/snakemake-wrappers/commit/26dbb9e5e5fa5f5454a470fb9000b254c4d77130)) * autobump bio/pyroe/idtoname ([#2274](https://www.github.com/snakemake/snakemake-wrappers/issues/2274)) ([76b9d89](https://www.github.com/snakemake/snakemake-wrappers/commit/76b9d8985f1a1d33b0815216404868e46b4c4d86)) * autobump bio/pyroe/makesplicedintronic ([#2255](https://www.github.com/snakemake/snakemake-wrappers/issues/2255)) ([436c1f8](https://www.github.com/snakemake/snakemake-wrappers/commit/436c1f8cd2a5a0674dbff22e24d02eb8aac1c855)) * autobump bio/pyroe/makeunspliceunspliced ([#2260](https://www.github.com/snakemake/snakemake-wrappers/issues/2260)) ([1da192d](https://www.github.com/snakemake/snakemake-wrappers/commit/1da192d80edc26fb03e8fa686cb40059ea535f35)) * autobump bio/ucsc/faToTwoBit ([#2286](https://www.github.com/snakemake/snakemake-wrappers/issues/2286)) ([93ba408](https://www.github.com/snakemake/snakemake-wrappers/commit/93ba4089edf02360c7ba1c195f76e4785e02a694)) * autobump bio/ucsc/twoBitToFa ([#2287](https://www.github.com/snakemake/snakemake-wrappers/issues/2287)) ([03447e8](https://www.github.com/snakemake/snakemake-wrappers/commit/03447e84d2184101967ad6bc75118a8cf1f28cf8)) --- 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
Fix issue #2292 and added new tests.
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,