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feat: allow for specifying multiple chromosomes in ensembl reference dna sequence download wrapper #2376
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johanneskoester
merged 4 commits into
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fet-allow-multiple-chroms-in-ensembl-ref-dna-download
Nov 23, 2023
Merged
feat: allow for specifying multiple chromosomes in ensembl reference dna sequence download wrapper #2376
johanneskoester
merged 4 commits into
master
from
fet-allow-multiple-chroms-in-ensembl-ref-dna-download
Nov 23, 2023
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…dna sequence download wrapper This will concatenate multiple chromosomes in the order in which they are listed under `params: chromosome:`.
johanneskoester
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Nov 23, 2023
johanneskoester
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November 23, 2023 08:57
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Nov 23, 2023
🤖 I have created a release \*beep\* \*boop\* --- ## [3.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.13.0...v3.0.0) (2023-11-23) ### ⚠ BREAKING CHANGES * replace all bbtool wrappers with one bbtool wrapper for all subcommands (#1322) ### Features * allow for specifying multiple chromosomes in ensembl reference dna sequence download wrapper ([#2376](https://www.github.com/snakemake/snakemake-wrappers/issues/2376)) ([c5590f0](https://www.github.com/snakemake/snakemake-wrappers/commit/c5590f03c9990b851181171e70217bb911ddac27)) * replace all bbtool wrappers with one bbtool wrapper for all subcommands ([#1322](https://www.github.com/snakemake/snakemake-wrappers/issues/1322)) ([6eb3c22](https://www.github.com/snakemake/snakemake-wrappers/commit/6eb3c227686c545b937d7cc5ef39b0b435f3e2b0)) ### Bug Fixes * Update MultiQC to 1.18 ([#2377](https://www.github.com/snakemake/snakemake-wrappers/issues/2377)) ([03bf2d9](https://www.github.com/snakemake/snakemake-wrappers/commit/03bf2d9e2d13968cb71a5e67d80a57b1502dc060)) ### Performance Improvements * autobump bio/bbtools ([#2325](https://www.github.com/snakemake/snakemake-wrappers/issues/2325)) ([bf09e80](https://www.github.com/snakemake/snakemake-wrappers/commit/bf09e801dba4e3cf2186ec80631e22df6adbf993)) * autobump bio/bedtools/bamtobed ([#2334](https://www.github.com/snakemake/snakemake-wrappers/issues/2334)) ([91b8054](https://www.github.com/snakemake/snakemake-wrappers/commit/91b8054fa408e2a96fed5ab24eea3f4f9f9a7f5c)) * autobump bio/bedtools/complement ([#2341](https://www.github.com/snakemake/snakemake-wrappers/issues/2341)) ([d0b9659](https://www.github.com/snakemake/snakemake-wrappers/commit/d0b96598864e0f5827eafb6a3f47aab8c2524995)) * autobump bio/bedtools/coveragebed ([#2342](https://www.github.com/snakemake/snakemake-wrappers/issues/2342)) ([8c25388](https://www.github.com/snakemake/snakemake-wrappers/commit/8c25388d851eaaae786f2ecdb3a684cf66037c1b)) * autobump bio/bedtools/genomecov ([#2336](https://www.github.com/snakemake/snakemake-wrappers/issues/2336)) ([2ba070e](https://www.github.com/snakemake/snakemake-wrappers/commit/2ba070edd0781b97227a2103bcd28670d0382141)) * autobump bio/bedtools/intersect ([#2338](https://www.github.com/snakemake/snakemake-wrappers/issues/2338)) ([b299438](https://www.github.com/snakemake/snakemake-wrappers/commit/b2994382ff94d11491ea991635fd25f74e9a56a4)) * autobump bio/bedtools/merge ([#2330](https://www.github.com/snakemake/snakemake-wrappers/issues/2330)) ([8c6ae83](https://www.github.com/snakemake/snakemake-wrappers/commit/8c6ae83bdd70b09dd3e434d13cc8b035ebe34089)) * autobump bio/bedtools/slop ([#2324](https://www.github.com/snakemake/snakemake-wrappers/issues/2324)) ([dfef51e](https://www.github.com/snakemake/snakemake-wrappers/commit/dfef51e5d5358a1fdfc87e7c560b31aab6e3a1aa)) * autobump bio/bedtools/sort ([#2328](https://www.github.com/snakemake/snakemake-wrappers/issues/2328)) ([fde082e](https://www.github.com/snakemake/snakemake-wrappers/commit/fde082e8c75bf674324499b52bd48340c0572f64)) * autobump bio/bedtools/split ([#2326](https://www.github.com/snakemake/snakemake-wrappers/issues/2326)) ([7663786](https://www.github.com/snakemake/snakemake-wrappers/commit/7663786a39a45ad0e6090324f400e94bb3e0bc68)) * autobump bio/blast/blastn ([#2335](https://www.github.com/snakemake/snakemake-wrappers/issues/2335)) ([518a30a](https://www.github.com/snakemake/snakemake-wrappers/commit/518a30ad707534046a2a1cfe861e861ece749683)) * autobump bio/blast/makeblastdb ([#2329](https://www.github.com/snakemake/snakemake-wrappers/issues/2329)) ([f24d810](https://www.github.com/snakemake/snakemake-wrappers/commit/f24d8106f4c2b6d1230535486967e82ae3f95dd5)) * autobump bio/bustools/count ([#2339](https://www.github.com/snakemake/snakemake-wrappers/issues/2339)) ([f8598f8](https://www.github.com/snakemake/snakemake-wrappers/commit/f8598f83cf8e4f7b5bd75f18bc036b4f9610de07)) * autobump bio/bwa-mem2/mem ([#2323](https://www.github.com/snakemake/snakemake-wrappers/issues/2323)) ([c751efd](https://www.github.com/snakemake/snakemake-wrappers/commit/c751efda5b93b155c1b42726dbe0f7fd4e10873c)) * autobump bio/bwa-meme/mem ([#2331](https://www.github.com/snakemake/snakemake-wrappers/issues/2331)) ([ae28cb4](https://www.github.com/snakemake/snakemake-wrappers/commit/ae28cb4db8473e147f033f447f186fead3a3f092)) * autobump bio/bwa-memx/mem ([#2337](https://www.github.com/snakemake/snakemake-wrappers/issues/2337)) ([1fe5ba7](https://www.github.com/snakemake/snakemake-wrappers/commit/1fe5ba7190b2f690a683a4c7f3397f039b8d71a2)) * autobump bio/bwa/mem ([#2333](https://www.github.com/snakemake/snakemake-wrappers/issues/2333)) ([e24ce7c](https://www.github.com/snakemake/snakemake-wrappers/commit/e24ce7c1affe9f779dd3bff9c72bfb46608fdbb9)) * autobump bio/bwa/sampe ([#2327](https://www.github.com/snakemake/snakemake-wrappers/issues/2327)) ([70a1ac3](https://www.github.com/snakemake/snakemake-wrappers/commit/70a1ac3efaeff35b3059e28d109ac8112b374669)) * autobump bio/bwa/samse ([#2332](https://www.github.com/snakemake/snakemake-wrappers/issues/2332)) ([61c0e6d](https://www.github.com/snakemake/snakemake-wrappers/commit/61c0e6d4fd93e13f956ef40720ab072519060d90)) * autobump bio/bwa/samxe ([#2340](https://www.github.com/snakemake/snakemake-wrappers/issues/2340)) ([d0865bc](https://www.github.com/snakemake/snakemake-wrappers/commit/d0865bc5a2f1e0a3358be2a678fd1545d95a75d8)) * autobump bio/cooltools/dots ([#2344](https://www.github.com/snakemake/snakemake-wrappers/issues/2344)) ([c55e268](https://www.github.com/snakemake/snakemake-wrappers/commit/c55e26814506ea5d6d33afd2689dfe005f2cf968)) * autobump bio/cooltools/eigs_cis ([#2348](https://www.github.com/snakemake/snakemake-wrappers/issues/2348)) ([1b7d26e](https://www.github.com/snakemake/snakemake-wrappers/commit/1b7d26e2775cdd6c785cf34a886e15bd82289aca)) * autobump bio/cooltools/eigs_trans ([#2346](https://www.github.com/snakemake/snakemake-wrappers/issues/2346)) ([f00f77b](https://www.github.com/snakemake/snakemake-wrappers/commit/f00f77b0a0d057f5576f1a375bc96b79a9e9f0c9)) * autobump bio/cooltools/expected_cis ([#2347](https://www.github.com/snakemake/snakemake-wrappers/issues/2347)) ([f4c8924](https://www.github.com/snakemake/snakemake-wrappers/commit/f4c8924b6b4f544a989e665d5e272d0f917ef700)) * autobump bio/cooltools/expected_trans ([#2350](https://www.github.com/snakemake/snakemake-wrappers/issues/2350)) ([7e3f763](https://www.github.com/snakemake/snakemake-wrappers/commit/7e3f7635a0a7e4832dbf4d45fcabb9497efb0e89)) * autobump bio/cooltools/insulation ([#2343](https://www.github.com/snakemake/snakemake-wrappers/issues/2343)) ([77e4ef5](https://www.github.com/snakemake/snakemake-wrappers/commit/77e4ef5d5a149bded23ebb28be3430e3c013eb76)) * autobump bio/cooltools/pileup ([#2345](https://www.github.com/snakemake/snakemake-wrappers/issues/2345)) ([6c6b0b1](https://www.github.com/snakemake/snakemake-wrappers/commit/6c6b0b1c6712d37909927f444debf13becb7841b)) * autobump bio/cooltools/saddle ([#2349](https://www.github.com/snakemake/snakemake-wrappers/issues/2349)) ([9f0f802](https://www.github.com/snakemake/snakemake-wrappers/commit/9f0f802f339667707bd8ed6013ca6e759ca9ce05)) * autobump bio/gseapy/gsea ([#2351](https://www.github.com/snakemake/snakemake-wrappers/issues/2351)) ([b3b3c94](https://www.github.com/snakemake/snakemake-wrappers/commit/b3b3c94d857cfcdfafdc9ef819ba8f2567f26afa)) * autobump bio/hmmer/hmmbuild ([#2355](https://www.github.com/snakemake/snakemake-wrappers/issues/2355)) ([2744f59](https://www.github.com/snakemake/snakemake-wrappers/commit/2744f59f5a9c13d5e80152f737d315535f4049ff)) * autobump bio/hmmer/hmmpress ([#2354](https://www.github.com/snakemake/snakemake-wrappers/issues/2354)) ([3f379bc](https://www.github.com/snakemake/snakemake-wrappers/commit/3f379bce4f20970983b319cd327bf5a31623ba8d)) * autobump bio/hmmer/hmmscan ([#2353](https://www.github.com/snakemake/snakemake-wrappers/issues/2353)) ([50c6425](https://www.github.com/snakemake/snakemake-wrappers/commit/50c642568ae259784c0fb50cf3440e3b84e0e6b5)) * autobump bio/hmmer/hmmsearch ([#2352](https://www.github.com/snakemake/snakemake-wrappers/issues/2352)) ([ed2bbcc](https://www.github.com/snakemake/snakemake-wrappers/commit/ed2bbccff232d5a16677ea60e6e70e241ed4bb61)) * autobump bio/last/lastal ([#2357](https://www.github.com/snakemake/snakemake-wrappers/issues/2357)) ([2589f18](https://www.github.com/snakemake/snakemake-wrappers/commit/2589f18971c2b377e0c8003c7f2ef7d412a277ae)) * autobump bio/last/lastdb ([#2356](https://www.github.com/snakemake/snakemake-wrappers/issues/2356)) ([4cee71f](https://www.github.com/snakemake/snakemake-wrappers/commit/4cee71f08cf1cf55c31ddb654f1349830412e708)) * autobump bio/picard/addorreplacereadgroups ([#2370](https://www.github.com/snakemake/snakemake-wrappers/issues/2370)) ([cf1cef0](https://www.github.com/snakemake/snakemake-wrappers/commit/cf1cef071e5b932c797078661bacf1eaf8ab12b2)) * autobump bio/picard/bedtointervallist ([#2360](https://www.github.com/snakemake/snakemake-wrappers/issues/2360)) ([b71d414](https://www.github.com/snakemake/snakemake-wrappers/commit/b71d414de9d5adea175fd773caead4c4e72a2dde)) * autobump bio/picard/collectalignmentsummarymetrics ([#2359](https://www.github.com/snakemake/snakemake-wrappers/issues/2359)) ([8873d75](https://www.github.com/snakemake/snakemake-wrappers/commit/8873d7552e8ef4acd58aa3d380e847768342aa59)) * autobump bio/picard/collectgcbiasmetrics ([#2366](https://www.github.com/snakemake/snakemake-wrappers/issues/2366)) ([f6d5248](https://www.github.com/snakemake/snakemake-wrappers/commit/f6d52486f7a511d705a383325ba07edd8821f99a)) * autobump bio/picard/collecthsmetrics ([#2369](https://www.github.com/snakemake/snakemake-wrappers/issues/2369)) ([f730d54](https://www.github.com/snakemake/snakemake-wrappers/commit/f730d54f21a56723237c33645f103645c9ea977e)) * autobump bio/picard/collectinsertsizemetrics ([#2373](https://www.github.com/snakemake/snakemake-wrappers/issues/2373)) ([a952ad4](https://www.github.com/snakemake/snakemake-wrappers/commit/a952ad4503ea74ecef60e0646c0fcbdc8aa8158f)) * autobump bio/picard/collectmultiplemetrics ([#2364](https://www.github.com/snakemake/snakemake-wrappers/issues/2364)) ([b21473a](https://www.github.com/snakemake/snakemake-wrappers/commit/b21473aff3482061b1e41b2b508f64e8072a77d7)) * autobump bio/picard/collectrnaseqmetrics ([#2361](https://www.github.com/snakemake/snakemake-wrappers/issues/2361)) ([2b36e3c](https://www.github.com/snakemake/snakemake-wrappers/commit/2b36e3c0dd38b1abd75e6a531c12913b4365b1b0)) * autobump bio/picard/collecttargetedpcrmetrics ([#2358](https://www.github.com/snakemake/snakemake-wrappers/issues/2358)) ([babe13e](https://www.github.com/snakemake/snakemake-wrappers/commit/babe13e9120377c7e6c3ea7f96c10fdb4e616571)) * autobump bio/picard/createsequencedictionary ([#2372](https://www.github.com/snakemake/snakemake-wrappers/issues/2372)) ([70630ac](https://www.github.com/snakemake/snakemake-wrappers/commit/70630ace2fba1b8a7e07e8dadeadb210dba5fbe6)) * autobump bio/picard/markduplicates ([#2365](https://www.github.com/snakemake/snakemake-wrappers/issues/2365)) ([66bea69](https://www.github.com/snakemake/snakemake-wrappers/commit/66bea6963e0cfe26908cd093acf011504869c4a3)) * autobump bio/picard/mergesamfiles ([#2362](https://www.github.com/snakemake/snakemake-wrappers/issues/2362)) ([b1e64e2](https://www.github.com/snakemake/snakemake-wrappers/commit/b1e64e2158f13381bd3c052e9641a1f6c65e9602)) * autobump bio/picard/mergevcfs ([#2363](https://www.github.com/snakemake/snakemake-wrappers/issues/2363)) ([2ca8f9e](https://www.github.com/snakemake/snakemake-wrappers/commit/2ca8f9eaa2255a7a9393e54ea88bae1c2d60ea06)) * autobump bio/picard/revertsam ([#2367](https://www.github.com/snakemake/snakemake-wrappers/issues/2367)) ([8a54527](https://www.github.com/snakemake/snakemake-wrappers/commit/8a54527a7b493d434c3d94e3376fab18673691b7)) * autobump bio/picard/samtofastq ([#2371](https://www.github.com/snakemake/snakemake-wrappers/issues/2371)) ([62ae9e5](https://www.github.com/snakemake/snakemake-wrappers/commit/62ae9e50d617a4529b767fce6d9f9b070d0dda45)) * autobump bio/picard/sortsam ([#2368](https://www.github.com/snakemake/snakemake-wrappers/issues/2368)) ([1a359a4](https://www.github.com/snakemake/snakemake-wrappers/commit/1a359a4bc88d38880bbf552698f95c6f1d605021)) * autobump bio/sortmerna ([#2374](https://www.github.com/snakemake/snakemake-wrappers/issues/2374)) ([e0920c9](https://www.github.com/snakemake/snakemake-wrappers/commit/e0920c9440f494167354f20583618d603b2c173e)) * autobump bio/vsearch ([#2375](https://www.github.com/snakemake/snakemake-wrappers/issues/2375)) ([c59fbc8](https://www.github.com/snakemake/snakemake-wrappers/commit/c59fbc8f52e16204ffb3b7c8b1c17479c4ebe391)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). 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This will concatenate multiple chromosomes in the order in which they are listed under
params: chromosome:
.Description
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,