ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2020-07-15T10:02:05+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/188[IlluminaWF]Hiding some analyses per defaut2020-07-15T10:02:05+02:00Audrey Gibert[IlluminaWF]Hiding some analyses per defautBy default, there is only the "log files" analysis that is hidden :
![image](/uploads/6603fbe0bddccccce2c13a16675d8079/image.png)
We should also hide
* Subset read files
* alignment
* alignmentStats
* InsertSizes
*...By default, there is only the "log files" analysis that is hidden :
![image](/uploads/6603fbe0bddccccce2c13a16675d8079/image.png)
We should also hide
* Subset read files
* alignment
* alignmentStats
* InsertSizes
* DemultiplexStatsV4 - MaintenanceAudrey GibertAudrey Gibert2021-07-01https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/193The purge process should ignore hidden runs and analyses2021-03-25T14:28:42+01:00Romain ThervilleThe purge process should ignore hidden runs and analysesWe don't want the hidden runs and analyzes to appear in the purge alert mail sent to the research teams.
So they have to be removed from the project's expired components, and excluded from the total storage size.We don't want the hidden runs and analyzes to appear in the purge alert mail sent to the research teams.
So they have to be removed from the project's expired components, and excluded from the total storage size.V3.2.7.5Romain ThervilleRomain Therville2021-03-05https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/186put the addrawfile component generic for any type of file to be saved2022-12-16T16:21:27+01:00Claire Kuchlyput the addrawfile component generic for any type of file to be savedNow the addrawfile component is only for fastq.gz files or with PacBio data we want to saves bam/xml and json files also.
So we want to add :
* [ ] management of any files to saved
* [ ] add calculation of the number of reads and base...Now the addrawfile component is only for fastq.gz files or with PacBio data we want to saves bam/xml and json files also.
So we want to add :
* [ ] management of any files to saved
* [ ] add calculation of the number of reads and bases for bam filesAudrey GibertAudrey Gibert2020-09-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/149[Sequel2] make new qc pipeline for Sequel2 data2022-12-16T16:21:28+01:00Claire Kuchly[Sequel2] make new qc pipeline for Sequel2 dataRaw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CL...Raw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CLR data : all files in output directory
Create of one analysis of run_stat.
? Make available fastq file.
?Claire KuchlyClaire Kuchly2020-01-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/148Add the duplicat rate without alignment in all illumina workflow2022-12-16T16:21:27+01:00Claire KuchlyAdd the duplicat rate without alignment in all illumina workflowAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyClaire KuchlyClaire Kuchly2019-12-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/137The static retention period given in the purge mail has to be computed2020-01-27T17:01:35+01:00Romain ThervilleThe static retention period given in the purge mail has to be computed"Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention..."Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention period.V3.2.6Romain ThervilleRomain Therville2019-11-21https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/112[ont-qc] Adding new analysis : Demultiplex Stat for ONT2021-03-25T13:39:09+01:00Maxime Manno[ont-qc] Adding new analysis : Demultiplex Stat for ONT#### We need to change the current demultiplex stat analysis management : :metal:
**What will change ?** replacement of porechop by Qcat, creation of a new analysis
* [x] Create new component
* [x] Create new template
* [x] Add seqki...#### We need to change the current demultiplex stat analysis management : :metal:
**What will change ?** replacement of porechop by Qcat, creation of a new analysis
* [x] Create new component
* [x] Create new template
* [x] Add seqkit stats logs for all the samples (included the unmappaed files)
* [x] Add fastq files only for the barcodes added into the pool
* [x] Add Qcat and Seqkit path and oprions into the application.propertiesV4 - MaintenanceMaxime MannoMaxime Manno2019-08-31https://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/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/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/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/16generate script to compute storage size for extention2019-07-23T14:15:59+02:00Celine Noirotgenerate script to compute storage size for extentionV3.1 - Purge2018-06-29https://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/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/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/246allow to create symlinks on genobioinfo2023-11-14T05:38:23+01:00Gerald Salingerald.salin@inra.frallow to create symlinks on genobioinfoallow to choose the server where to create the cymbolic links (genologin pr genobioinfo)allow to choose the server where to create the cymbolic links (genologin pr genobioinfo)V3.4.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/245store ngl-bi analysis code in ng6 run2024-03-11T10:40:45+01:00Gerald Salingerald.salin@inra.frstore ngl-bi analysis code in ng6 runto allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflowto allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflowV3.4.5Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/239error displaying workflow status if too much runs present2022-11-07T16:33:55+01:00Gerald Salingerald.salin@inra.frerror displaying workflow status if too much runs presenterror in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.error in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.V3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr