ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-07-23T09:22:06+02:00https://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/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/113[ont_qc] Add N90 and 5 longest reads informations2019-07-24T09:39:10+02:00Maxime Manno[ont_qc] Add N90 and 5 longest reads informationsV3.2.3.1Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/227[ont_qc] Change end of sequencing report file2022-05-11T10:29:03+02:00Jules Sabban[ont_qc] Change end of sequencing report fileNanopore has change the end of sequencing report file format from PDF to HTMLNanopore has change the end of sequencing report file format from PDF to HTMLV3.3Jules SabbanJules Sabbanhttps://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/225[Purge] Do not purge the hidden runs and analyses2022-04-26T14:00:23+02:00Romain Therville[Purge] Do not purge the hidden runs and analysesHidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)Hidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/179[purge] link analyzes to runs in the email2021-10-12T08:53:41+02:00Gerald Salingerald.salin@inra.fr[purge] link analyzes to runs in the emailFiles impacted of:
• Runs : NemaTools-1 (12035), NemaTools-1 (12336)
• Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035), IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)
...Files impacted of:
• Runs : NemaTools-1 (12035), NemaTools-1 (12336)
• Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035), IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)
to be transformed as
Files impacted of:
• Run NemaTools-1 (12035)
Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035),
• Run NemaTools-1 (12336)
Analyzes : IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)V3.4Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/182[Web interface]Improve FAQ accesses2021-09-01T08:59:46+02:00Audrey Gibert[Web interface]Improve FAQ accesses2 ideas on the web interface :
* [x] on a project page, on the top-right corner below the data overview frame : adding a sentence "You can add a collaborator to your project : visit the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id...2 ideas on the web interface :
* [x] on a project page, on the top-right corner below the data overview frame : adding a sentence "You can add a collaborator to your project : visit the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id=57) > How to add a user to my project?
* [x] On the run view, in the Raw Data tab, below the "Retention date" frame : adding "There is a fast way to retrieve your data, more information in the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id=57) > How to get my data?
* [x] On an analysis view, in the Download section, same sentence as above : "You can retrieve your data easily, more information in the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id=57) > How to get my data?
* [x] Be more explicit with the download by URL on windows in the FAQ
- [x] @gsalin : Add a news to signal the information!V3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/161A rework of the purge processes is needed2020-03-04T09:25:59+01:00Romain ThervilleA rework of the purge processes is neededWith the new retention, space and migration features, a few new cases have to be handled by the purge system:
* New mail model, for the projects in shortterm storage (4 months), that indicate 1 month in advance that the data are going ...With the new retention, space and migration features, a few new cases have to be handled by the purge system:
* New mail model, for the projects in shortterm storage (4 months), that indicate 1 month in advance that the data are going to be deleted.
No extention is allowed in this case.
* A new CRON that sends the purge mail one month before the data deletion and opens a purge request (Admin > Mail obsolete projects).
* A new CRON (every week) to send to the ng6 administrators the list of the last purge mails sent.V3.2.7Romain ThervilleRomain Thervillehttps://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/214add a link to the reinit password interface2021-10-12T08:47:06+02:00Gerald Salingerald.salin@inra.fradd a link to the reinit password interfaceV3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/126Add a new group superadmin2019-10-29T09:36:55+01:00Celine NoirotAdd a new group superadminDuring purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interest...During purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interesting to have a new group "superadmin" which give access to all the projects.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/151Add a space id column in Administration > Mail obsolete project2020-01-16T17:33:08+01:00Romain ThervilleAdd a space id column in Administration > Mail obsolete project- New space_id column
- Replace the "size greater than" filter with a "space_id" selection- New space_id column
- Replace the "size greater than" filter with a "space_id" selectionV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/69Add a super admin ng6 who can see all projects2019-09-27T13:14:15+02:00Claire KuchlyAdd a super admin ng6 who can see all projectshttps://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/117Add duplication stat to alignmentStat analyze2019-08-30T13:23:44+02:00Claire KuchlyAdd duplication stat to alignmentStat analyzeV3.2.5Natacha FaivreNatacha Faivrehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/31add link and name to runs and analyses and projects in the purge email2019-09-10T11:58:20+02:00Gerald Salingerald.salin@inra.fradd link and name to runs and analyses and projects in the purge emaile.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,585...e.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,5855,5845,6309,6310,6311,6313,6314,6320,6321,6382,6381,6380,6379,6378,6383,6758,6757,6759,6763,8532,8539,8544,8547,8559,8568,8571,8582,158V3.2.6Romain ThervilleRomain Thervillehttps://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/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/233add support to typo3 v112022-10-07T17:07:41+02:00Gerald Salingerald.salin@inra.fradd support to typo3 v11typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11V3.4Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr