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feat: DeseqDataSet from multiple input #1326
Merged
johanneskoester
merged 66 commits into
snakemake:master
from
tdayris:deseq2-from-tximport
May 12, 2023
Merged
feat: DeseqDataSet from multiple input #1326
johanneskoester
merged 66 commits into
snakemake:master
from
tdayris:deseq2-from-tximport
May 12, 2023
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* perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml.
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* Add autobump action * fix paths * dbg * dbg branch * add checkout * dbg * trigger rerun * entity regex and add label * dbg * Update autobump.yml * Update autobump.yml
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fgvieira
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May 4, 2023
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
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reviewed
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🤖 I have created a release \*beep\* \*boop\* --- ## [1.30.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.29.0...v1.30.0) (2023-05-12) ### Features * add memory inference to samtools sort ([#1208](https://www.github.com/snakemake/snakemake-wrappers/issues/1208)) ([d70a806](https://www.github.com/snakemake/snakemake-wrappers/commit/d70a80650c640ab37e21690bd9c90dc581d2ec4e)) * deeptools bamcoverage ([#1237](https://www.github.com/snakemake/snakemake-wrappers/issues/1237)) ([ee2413b](https://www.github.com/snakemake/snakemake-wrappers/commit/ee2413b7f4e5576692330821f3cdd8829d731144)) * deeptools plotcoverage ([#1241](https://www.github.com/snakemake/snakemake-wrappers/issues/1241)) ([d08e4c6](https://www.github.com/snakemake/snakemake-wrappers/commit/d08e4c6908347ff979ff512f6523368ed9fc0df2)) * DeseqDataSet from multiple input ([#1326](https://www.github.com/snakemake/snakemake-wrappers/issues/1326)) ([25d8a07](https://www.github.com/snakemake/snakemake-wrappers/commit/25d8a076bc6830bfcf58d7a5999b68a790879f9a)) * Gffread ([#1291](https://www.github.com/snakemake/snakemake-wrappers/issues/1291)) ([d613ddf](https://www.github.com/snakemake/snakemake-wrappers/commit/d613ddffa7f78f5697e836e71ce2e51f232c1884)) * Salmon-Tximport meta-wrapper ([#1270](https://www.github.com/snakemake/snakemake-wrappers/issues/1270)) ([1e31da2](https://www.github.com/snakemake/snakemake-wrappers/commit/1e31da29769eebefdff470ae24598eb479547bca)) ### Bug Fixes * auto memory calculation ([#1210](https://www.github.com/snakemake/snakemake-wrappers/issues/1210)) ([b08081f](https://www.github.com/snakemake/snakemake-wrappers/commit/b08081fc066b10040fcd94a8f9fd1b70099a6f54)) * ensembl annotation GRCh37 gft release ([#1296](https://www.github.com/snakemake/snakemake-wrappers/issues/1296)) ([d5be001](https://www.github.com/snakemake/snakemake-wrappers/commit/d5be001cfdd5cd85fdbd19abe15de43310f9bfed)) * fixed bug when formatting string in GATK denoisereadcounts ([#1343](https://www.github.com/snakemake/snakemake-wrappers/issues/1343)) ([8cc5d91](https://www.github.com/snakemake/snakemake-wrappers/commit/8cc5d91f0b459ef18d461367a449c9bf5c901571)) ### Performance Improvements * autobump bio/bcftools/call ([#1349](https://www.github.com/snakemake/snakemake-wrappers/issues/1349)) ([064d4a4](https://www.github.com/snakemake/snakemake-wrappers/commit/064d4a469e8a3be063c7ac2b4916127c1f4b9abf)) * autobump bio/bcftools/reheader ([#1362](https://www.github.com/snakemake/snakemake-wrappers/issues/1362)) ([bc4bb1d](https://www.github.com/snakemake/snakemake-wrappers/commit/bc4bb1deb95a5cab588c34b55e03496a5242dcf3)) * autobump bio/bcftools/stats ([#1361](https://www.github.com/snakemake/snakemake-wrappers/issues/1361)) ([444b198](https://www.github.com/snakemake/snakemake-wrappers/commit/444b198e0a97483ce66011a0cb022166d6d45ed2)) * autobump bio/bedtools/genomecov ([#1351](https://www.github.com/snakemake/snakemake-wrappers/issues/1351)) ([f39d37d](https://www.github.com/snakemake/snakemake-wrappers/commit/f39d37dd38dc6a1e672b901278cf8774a132f4c2)) * autobump bio/bedtools/merge ([#1348](https://www.github.com/snakemake/snakemake-wrappers/issues/1348)) ([46ba353](https://www.github.com/snakemake/snakemake-wrappers/commit/46ba35317bd292816fbc833ca43b2bc50485a0a9)) * autobump bio/bedtools/sort ([#1357](https://www.github.com/snakemake/snakemake-wrappers/issues/1357)) ([e17cb5a](https://www.github.com/snakemake/snakemake-wrappers/commit/e17cb5a405d0d770749969cd89a0bcc58179f292)) * autobump bio/bismark/bam2nuc ([#1341](https://www.github.com/snakemake/snakemake-wrappers/issues/1341)) ([ce2b39e](https://www.github.com/snakemake/snakemake-wrappers/commit/ce2b39e65752a5088088c65d67abe3fa4d01a0dc)) * autobump bio/bismark/bismark2report ([#1334](https://www.github.com/snakemake/snakemake-wrappers/issues/1334)) ([d497124](https://www.github.com/snakemake/snakemake-wrappers/commit/d497124a689d436169dd360e674bd7af7bfc7fa9)) * autobump bio/bowtie2/align ([#1356](https://www.github.com/snakemake/snakemake-wrappers/issues/1356)) ([0e6cc68](https://www.github.com/snakemake/snakemake-wrappers/commit/0e6cc68ed2499215903a1adb1e83c883f6d73277)) * autobump bio/busco ([#1359](https://www.github.com/snakemake/snakemake-wrappers/issues/1359)) ([41f1185](https://www.github.com/snakemake/snakemake-wrappers/commit/41f1185ee23cd2810022510a2d89f4ea39212a44)) * autobump bio/bwa/samxe ([#1335](https://www.github.com/snakemake/snakemake-wrappers/issues/1335)) ([8042216](https://www.github.com/snakemake/snakemake-wrappers/commit/80422161ea03b1d8a1f513f7562b7cbe6667a952)) * autobump bio/deeptools/plotfingerprint ([#1345](https://www.github.com/snakemake/snakemake-wrappers/issues/1345)) ([39f88b7](https://www.github.com/snakemake/snakemake-wrappers/commit/39f88b73d148b02436d7476642ca24b02201e6d6)) * autobump bio/gatk/applybqsr ([#1339](https://www.github.com/snakemake/snakemake-wrappers/issues/1339)) ([ec62a41](https://www.github.com/snakemake/snakemake-wrappers/commit/ec62a41f3ece28922bc9a35edec5c44997006320)) * autobump bio/gatk/splitncigarreads ([#1350](https://www.github.com/snakemake/snakemake-wrappers/issues/1350)) ([7a7eb1e](https://www.github.com/snakemake/snakemake-wrappers/commit/7a7eb1e46b65843a295055c6cd74fe49ee68466c)) * autobump bio/gatk/variantfiltration ([#1340](https://www.github.com/snakemake/snakemake-wrappers/issues/1340)) ([d108c9c](https://www.github.com/snakemake/snakemake-wrappers/commit/d108c9c0adc28b8b7bac14b418f1f79df91a90a5)) * autobump bio/manta ([#1342](https://www.github.com/snakemake/snakemake-wrappers/issues/1342)) ([a23858a](https://www.github.com/snakemake/snakemake-wrappers/commit/a23858aa5e6980e559ee8cb02f0a54208af9eef5)) * autobump bio/minimap2/aligner ([#1329](https://www.github.com/snakemake/snakemake-wrappers/issues/1329)) ([45c53eb](https://www.github.com/snakemake/snakemake-wrappers/commit/45c53eba9041a28745c2d678638827b0b2537667)) * autobump bio/open-cravat/run ([#1330](https://www.github.com/snakemake/snakemake-wrappers/issues/1330)) ([fc82508](https://www.github.com/snakemake/snakemake-wrappers/commit/fc82508898e6de6c5f673f1a3044bda7fe02d656)) * autobump bio/picard/addorreplacereadgroups ([#1333](https://www.github.com/snakemake/snakemake-wrappers/issues/1333)) ([d273596](https://www.github.com/snakemake/snakemake-wrappers/commit/d27359682dbe2a4c411971e09c72079a9d803dfb)) * autobump bio/picard/collectinsertsizemetrics ([#1352](https://www.github.com/snakemake/snakemake-wrappers/issues/1352)) ([ae1e2bd](https://www.github.com/snakemake/snakemake-wrappers/commit/ae1e2bd62f7a6683c495abc70cd9dd1773b683f4)) * autobump bio/rasusa ([#1353](https://www.github.com/snakemake/snakemake-wrappers/issues/1353)) ([3c41241](https://www.github.com/snakemake/snakemake-wrappers/commit/3c4124152e9b49bd02f944707e47517d6e7826dc)) * autobump bio/samtools/fastx ([#1347](https://www.github.com/snakemake/snakemake-wrappers/issues/1347)) ([d6e6329](https://www.github.com/snakemake/snakemake-wrappers/commit/d6e63291192027c7c4c994d8d5e2dee6f727b5cb)) * autobump bio/seqkit/fx2tab ([#1338](https://www.github.com/snakemake/snakemake-wrappers/issues/1338)) ([53922ca](https://www.github.com/snakemake/snakemake-wrappers/commit/53922ca8c2a7ad2da5c17a39fb98e724dff56df5)) * autobump bio/snpeff/annotate ([#1363](https://www.github.com/snakemake/snakemake-wrappers/issues/1363)) ([9ba0b3d](https://www.github.com/snakemake/snakemake-wrappers/commit/9ba0b3ddd02f784df8eddd203a5619362c88f36f)) * autobump bio/snpeff/download ([#1358](https://www.github.com/snakemake/snakemake-wrappers/issues/1358)) ([2c5a385](https://www.github.com/snakemake/snakemake-wrappers/commit/2c5a385ad1d499d183a6075d1c274d7beab14621)) * autobump bio/sourmash/compute ([#1360](https://www.github.com/snakemake/snakemake-wrappers/issues/1360)) ([1ec19c2](https://www.github.com/snakemake/snakemake-wrappers/commit/1ec19c22df58905271b50399b8b1d83e94801fe3)) * autobump bio/sra-tools/fasterq-dump ([#1355](https://www.github.com/snakemake/snakemake-wrappers/issues/1355)) ([d1118bd](https://www.github.com/snakemake/snakemake-wrappers/commit/d1118bd4f59c1315b99539c8b2d99bb1ac86326c)) * autobump bio/tabix/index ([#1336](https://www.github.com/snakemake/snakemake-wrappers/issues/1336)) ([dfab9c6](https://www.github.com/snakemake/snakemake-wrappers/commit/dfab9c6aa5e50596d7348553d8414c534130f5f8)) * autobump bio/vembrane/table ([#1337](https://www.github.com/snakemake/snakemake-wrappers/issues/1337)) ([953c0dc](https://www.github.com/snakemake/snakemake-wrappers/commit/953c0dcdedc8ebbaff96e139c93d5c2aef3ad87f)) * autobump bio/vep/plugins ([#1346](https://www.github.com/snakemake/snakemake-wrappers/issues/1346)) ([887ba11](https://www.github.com/snakemake/snakemake-wrappers/commit/887ba11f0be215ddf0110d6ba31de4a0eb93056c)) * autobump bio/vg/sim ([#1332](https://www.github.com/snakemake/snakemake-wrappers/issues/1332)) ([91574fd](https://www.github.com/snakemake/snakemake-wrappers/commit/91574fd8795d55ff9e60b35f884c4f2cd7956b54)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). 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Description
This PR adds a wrapper to build DESeqDataSets for DESeq2, from multiple sources (tximport, ranged SE, TSV/R count matrices, already existing DESeqDataSet), and (on user request) performs both releveling and count filtering as DESeq2 documentation suggests.
If you think this should be broken into multiple separate wrappers, please let me know, I'll close this PR and submit the separated sub-functions one by one.
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,