ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2018-06-19T15:14:21+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/3Infos générales sur la page purge2018-06-19T15:14:21+02:00Celine NoirotInfos générales sur la page purgeDonner l'information de :
- la somme totale "purgeable"
- le nombre total de projets
correspondant aux projets filtrés.Donner l'information de :
- la somme totale "purgeable"
- le nombre total de projets
correspondant aux projets filtrés.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-04-18https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/23Add total project size in purge demand email2018-06-27T16:32:07+02:00Celine NoirotAdd total project size in purge demand emailV3.1 - PurgeCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/18List all project even not obsolete2018-06-28T18:11:30+02:00Celine NoirotList all project even not obsoleteList all project in purge management to enable the extention for the projects of a complete lab.List all project in purge management to enable the extention for the projects of a complete lab.V3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/17Add project extention2018-07-18T15:48:10+02:00Celine NoirotAdd project extentionIf a project has a obsolete run (not all), all its run or analysis can be extentedIf a project has a obsolete run (not all), all its run or analysis can be extentedV3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/12Add visualisation and compute of stored/purged size per group/lab2018-07-18T15:48:10+02:00Celine NoirotAdd visualisation and compute of stored/purged size per group/labAdd visualisation of stored/purged size per group/lab
Generate a table and a graphics.Add visualisation of stored/purged size per group/lab
Generate a table and a graphics.V3.1 - PurgeCeline NoirotCeline Noirot2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/13flag project which all runs and analyses are purgeable2018-07-18T15:48:10+02:00Claire Kuchlyflag project which all runs and analyses are purgeableV3.1 - PurgeClaire KuchlyClaire Kuchly2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/7Update of Samtools2018-08-01T09:19:30+02:00Maxime MannoUpdate of SamtoolsOn Genotoul we use samtools v1.1
We want to use the v1.3.1 on genologin (for the momentOn Genotoul we use samtools v1.1
We want to use the v1.3.1 on genologin (for the momentV3.2 - SlurmMaxime MannoMaxime Manno2018-04-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/6Update of the picardtools2018-08-02T13:07:23+02:00Audrey GibertUpdate of the picardtoolsWe have picardtools 1.88
we want to test v2.14 on SLURMWe have picardtools 1.88
we want to test v2.14 on SLURMV3.2 - SlurmAudrey GibertAudrey Gibert2018-04-27https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/32add manual for purging data2018-08-02T14:57:31+02:00Gerald Salingerald.salin@inra.fradd manual for purging dataV4 - MaintenanceClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/42Upgrade jflow: load server file2018-08-09T17:15:33+02:00Celine NoirotUpgrade jflow: load server filecheck how ng6 upload server file.
This functionnality is now in jflowcheck how ng6 upload server file.
This functionnality is now in jflowV3.2 - SlurmCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/29Modification du plugin nG6 typo3 pour utilisation sur php7 et typo3 V82018-08-28T14:15:29+02:00Gerald Salingerald.salin@inra.frModification du plugin nG6 typo3 pour utilisation sur php7 et typo3 V8copier/coller du mail ne fonctionne pas très bien.
mise de la procedure de mise à jour du plugin ng6 en PJ[procedure_mise_a_jour_ng6_typo3V8.pdf](/uploads/99473730dc54cc392fe051dc18a6f72e/procedure_mise_a_jour_ng6_typo3V8.pdf)[diffModifn...copier/coller du mail ne fonctionne pas très bien.
mise de la procedure de mise à jour du plugin ng6 en PJ[procedure_mise_a_jour_ng6_typo3V8.pdf](/uploads/99473730dc54cc392fe051dc18a6f72e/procedure_mise_a_jour_ng6_typo3V8.pdf)[diffModifnG6_Typo3_V8](/uploads/899e4ad5977dafc9bf0558339e03f93f/diffModifnG6_Typo3_V8)V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/14[purge] : for projet who has no administror : mail sent to all users project2018-08-28T14:39:30+02:00Claire Kuchly[purge] : for projet who has no administror : mail sent to all users projectV3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/66add a way to align illumina reads against a subset of reads2018-09-06T13:56:45+02:00Gerald Salingerald.salin@inra.fradd a way to align illumina reads against a subset of readswith novaseq/hiseq data, the alignment step can be very time consuming.
think of a way to only align a subset of the reads, giving a workflow argument, e.g. --align-subset-reads
some source code is available in the extract_random_seq f...with novaseq/hiseq data, the alignment step can be very time consuming.
think of a way to only align a subset of the reads, giving a workflow argument, e.g. --align-subset-reads
some source code is available in the extract_random_seq function of SubSetAssignation componentV3.2 - SlurmClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/71clean pipeline outputs if succeeded2018-09-06T15:09:01+02:00Gerald Salingerald.salin@inra.frclean pipeline outputs if succeededallow the deletion of files in the worflow output dir to save dik spaceallow the deletion of files in the worflow output dir to save dik spaceV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/68add md5sum for raw data in all pipelines2018-09-07T12:07:23+02:00Gerald Salingerald.salin@inra.fradd md5sum for raw data in all pipelinesV3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/70enhance disk usage with concatenatefilesgroups2018-09-17T09:30:51+02:00Gerald Salingerald.salin@inra.frenhance disk usage with concatenatefilesgroupsto limit the disk usage in illumina pipelines, do not store the output of ConcatenateFilesGroups component in its out output folder, but rather in the run.get_work_directory() folder.
saves a copy step (originally done in AddRawFiles com...to limit the disk usage in illumina pipelines, do not store the output of ConcatenateFilesGroups component in its out output folder, but rather in the run.get_work_directory() folder.
saves a copy step (originally done in AddRawFiles componenent) and limit the disk usage (can represent few hundreds of Gb for novaseq runs)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/96Extra space between md5 and file name in md5sum.txt2018-12-14T18:44:42+01:00Roxane BoyerExtra space between md5 and file name in md5sum.txtThere are 3 spaces instead of 2 in the md5sum file :
```
3efa244db27854b63b740a31e16e85e6 ESE00019_AAGTCCAA-TACTCATA-AH2MC2BBXY_L002_R1.fastq.gz
ff0510e4615e75a5b5cccac402262e88 ESE00107_GTTCCAAT-GCAGAATT-AH2MC2BBXY_L002_R2.fastq.gz...There are 3 spaces instead of 2 in the md5sum file :
```
3efa244db27854b63b740a31e16e85e6 ESE00019_AAGTCCAA-TACTCATA-AH2MC2BBXY_L002_R1.fastq.gz
ff0510e4615e75a5b5cccac402262e88 ESE00107_GTTCCAAT-GCAGAATT-AH2MC2BBXY_L002_R2.fastq.gz
```
md5sum -c md5sum.txt
md5sum: PLF7_GCCGCG-C28GH_L001_R1.fastq.gz: Aucun fichier ou dossier de ce type
PLF7_GCCGCG-C28GH_L001_R1.fastq.gz : Échec d'ouverture ou de lecture.Roxane BoyerRoxane Boyerhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/101adapt visualisation of ONT versions (gridion and promethion)2019-01-15T14:01:26+01:00Maxime Mannoadapt visualisation of ONT versions (gridion and promethion)The scripts parse-version for ONT gridion and promethion have been modified. We need to update and adapt the visualisationThe scripts parse-version for ONT gridion and promethion have been modified. We need to update and adapt the visualisationV3.2.3Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/111[ont-qc] Adding logs to ont-qc analysis2019-07-23T09:22:06+02:00Maxime Manno[ont-qc] Adding logs to ont-qc analysis#### It should have log files from :
* [x] the Merkaat pipeline log
* [x] final status run summary log#### It should have log files from :
* [x] the Merkaat pipeline log
* [x] final status run summary logV3.2.4Maxime MannoMaxime Manno2019-07-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/16generate script to compute storage size for extention2019-07-23T14:15:59+02:00Celine Noirotgenerate script to compute storage size for extentionV3.1 - Purge2018-06-29