metagWGS merge requestshttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests2023-06-02T21:33:09+02:00https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/26v2.4.22023-06-02T21:33:09+02:00Claire Hoedev2.4.2fix bug in binette and add checkm2 parameterfix bug in binette and add checkm2 parameterClaire HoedeClaire Hoedehttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/25V2.4 Add coassembly and replace bin refinement with binette2023-01-26T16:24:35+01:00VIENNE MAINAV2.4 Add coassembly and replace bin refinement with binetteFix some issues
Update docs
Add coassembly
Replace bin refinement with binetteFix some issues
Update docs
Add coassembly
Replace bin refinement with binetteV2.4 - Various workflows and documentation improvmentsVIENNE MAINAVIENNE MAINAhttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/24manage coassembly for step 22023-01-10T16:15:20+01:00VIENNE MAINAmanage coassembly for step 2Adds coassembly and some fixesAdds coassembly and some fixesVIENNE MAINAVIENNE MAINAhttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/23Remove prokka2022-10-27T10:54:52+02:00Ghost UserRemove prokkasee issue #163see issue #163VIENNE MAINAVIENNE MAINAhttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/22Hotfix for metagWGS v3.2.12022-10-27T10:46:02+02:00Ghost UserHotfix for metagWGS v3.2.1This is a merge request for metagWGSv 3.2.1
What has changed?
* Fix remaining conflicts from last realease
* Update documentation
* Fix sample name in taxonomic affiliation plots
* Update multiqc config #210
* Add header to metaWRAP...This is a merge request for metagWGSv 3.2.1
What has changed?
* Fix remaining conflicts from last realease
* Update documentation
* Fix sample name in taxonomic affiliation plots
* Update multiqc config #210
* Add header to metaWRAP scriptshttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/21Do checkpoint on values after Cdhit #302022-08-18T09:32:12+02:00Celine NoirotDo checkpoint on values after Cdhit #30Issues en vracCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/20Adding possibility to give flowcell information on samplesheet2022-07-26T10:51:17+02:00VIENNE MAINAAdding possibility to give flowcell information on samplesheetPermet la gestion d'échantillon sequencé sur differentes flowcell
Ajoute l'utilisation de metadata dans les channels avec les reads/inputsPermet la gestion d'échantillon sequencé sur differentes flowcell
Ajoute l'utilisation de metadata dans les channels avec les reads/inputshttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/19Jean.mainguy master patch 097972022-05-30T16:57:19+02:00Ghost UserJean.mainguy master patch 09797https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/18Revert "Merge branch 'jean.mainguy-master-patch-09797' into 'master'"2022-05-30T16:55:13+02:00Ghost UserRevert "Merge branch 'jean.mainguy-master-patch-09797' into 'master'"This reverts merge request !17This reverts merge request !17https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/17add description of top taxon output added in commit 2e1644f51400ebdd514fe538b...2022-05-30T16:54:37+02:00Ghost Useradd description of top taxon output added in commit 2e1644f51400ebdd514fe538b9ba16e39a06cbde #185https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/16Devel2022-02-01T14:18:44+01:00Ghost UserDevelFix code error in aln2taxaffi.py that was generating the final plots over and over in a for loop along contig analysis affecting the overall performance of the script.Fix code error in aln2taxaffi.py that was generating the final plots over and over in a for loop along contig analysis affecting the overall performance of the script.https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/15DSL22022-01-14T10:57:03+01:00Celine NoirotDSL2DSL2 version
- pass to DSL2 to get 2 workflow (Short-read and HiFi)
- gene are named with feature (prot/rrna)
- aln2taxaffi.py refactored to use new_taxdump and prot.accession2taxid.FULL
- add header in diamond output and use it while p...DSL2 version
- pass to DSL2 to get 2 workflow (Short-read and HiFi)
- gene are named with feature (prot/rrna)
- aln2taxaffi.py refactored to use new_taxdump and prot.accession2taxid.FULL
- add header in diamond output and use it while parsing
- replace mosdepth by samtools coverage
- replace bedtools bamtofastq by samtools fastq
- check gff valididy after prokka
- simplify config files
- upadate documentation
- chunk assambly to reduce process time of filtering stepV2.2 DSL2 transitionCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/13DSL2 version2022-01-14T10:51:16+01:00Celine NoirotDSL2 versionMerge new DSL2 versionMerge new DSL2 versionV2.2 DSL2 transitionCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/14Dev docs2022-01-14T09:39:53+01:00Celine NoirotDev docsMaina work to mergeMaina work to mergeV2.2 DSL2 transitionCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/12Merge dsl2 in dev to finalize dsl1 to dsl2 transition2021-12-13T17:22:49+01:00MARTIN PierreMerge dsl2 in dev to finalize dsl1 to dsl2 transitionChanged MetagWGS from DSL1 to DSL2
Added Hifi data treatment
Implemented samplesheet usage
Implemented various issues from DSL1 and DSL2
Updated documentation with changes made to MetagWGSChanged MetagWGS from DSL1 to DSL2
Added Hifi data treatment
Implemented samplesheet usage
Implemented various issues from DSL1 and DSL2
Updated documentation with changes made to MetagWGSV2.2 DSL2 transitionMARTIN PierreMARTIN Pierrehttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/11MR before tag 2.12021-09-27T11:38:59+02:00MARTIN PierreMR before tag 2.1merge request before tag 2.1
changelog creationmerge request before tag 2.1
changelog creationV2.1 Tests fonctionnelsMARTIN PierreMARTIN Pierrehttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/10MR before tag 2.12021-09-27T11:20:13+02:00MARTIN PierreMR before tag 2.1changes to documentationchanges to documentationV2.1 Tests fonctionnelsMARTIN PierreMARTIN Pierrehttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/9Functional tests implementation + refactoring + documentation2021-09-16T14:29:20+02:00MARTIN PierreFunctional tests implementation + refactoring + documentationImplementation of functional tests for metagwgs.
Refactoring of various issues.
Documentation updates.Implementation of functional tests for metagwgs.
Refactoring of various issues.
Documentation updates.Issues en vracMARTIN PierreMARTIN Pierrehttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/8Merge dev into master for version 2.0.2021-02-25T11:14:25+01:00Joanna FourquetMerge dev into master for version 2.0.V2.0Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/merge_requests/7Merge dev into master for version 2.0.2021-02-24T14:41:57+01:00Joanna FourquetMerge dev into master for version 2.0.V2.0Celine NoirotCeline Noirot