ng6 merge requestshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests2019-10-10T13:48:38+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/48N g6 ont demultiplex2019-10-10T13:48:38+02:00Maxime MannoN g6 ont demultiplexV3.2.6Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/51Issue#1202019-10-10T15:51:37+02:00Romain ThervilleIssue#120Adds a new retention policy line in the single project view display.
For more informations, check https://forgemia.inra.fr/genotoul-bioinfo/ng6/issues/120 .Adds a new retention policy line in the single project view display.
For more informations, check https://forgemia.inra.fr/genotoul-bioinfo/ng6/issues/120 .V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/50Ng6 slurm 10 x2019-10-10T16:51:42+02:00Claire KuchlyNg6 slurm 10 xAdd illumuna_qc_10X pipelines to ng6Add illumuna_qc_10X pipelines to ng6V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/52Issue#1292019-10-14T13:22:08+02:00Romain ThervilleIssue#129There was a bug concerning the moved files's directories. It has been fixed, and some logging calls have been removed.There was a bug concerning the moved files's directories. It has been fixed, and some logging calls have been removed.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/53Merge branch issue#120 with master2019-10-17T09:54:48+02:00Romain ThervilleMerge branch issue#120 with masterThe displayed date (when the retention is a fixed date) in project view was wrong.
Issue #120The displayed date (when the retention is a fixed date) in project view was wrong.
Issue #120V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/54merge branch issue#129 with master2019-10-17T09:54:56+02:00Romain Thervillemerge branch issue#129 with masterThe workflow has been re-writed to put most of the BD treatments in the
corresponding classes (Run, Analysis, Project).
issue#129The workflow has been re-writed to put most of the BD treatments in the
corresponding classes (Run, Analysis, Project).
issue#129V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/55merge branch issue#95 with master2019-10-17T09:57:00+02:00Romain Thervillemerge branch issue#95 with masterFix for jflow.min.js
Resolves the addanalysis bug
issue#95, issue#85Fix for jflow.min.js
Resolves the addanalysis bug
issue#95, issue#85V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/56Merge branch issue#129 with master2019-10-17T10:39:18+02:00Romain ThervilleMerge branch issue#129 with masterEnhancement for the workflow 'switch_project_space_id'
I have moved the DB updates down in the code, to only register
migrations that went well.
issue #129Enhancement for the workflow 'switch_project_space_id'
I have moved the DB updates down in the code, to only register
migrations that went well.
issue #129V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/57Merge branch issue#126 with master2019-10-17T14:40:49+02:00Romain ThervilleMerge branch issue#126 with masterIssue#126
* The superadmin group allows to navigate every project, run and analysis on nG6, hidden or not, with admin rights.
* There is a new table in the admin section ( Administration > Admin management ) that allow superadmins to ad...Issue#126
* The superadmin group allows to navigate every project, run and analysis on nG6, hidden or not, with admin rights.
* There is a new table in the admin section ( Administration > Admin management ) that allow superadmins to add and remove users to and from the superadmin group.
* The group's key is NEVER written directly in the source code, allowing an easier deployment for production use.
* The only requirement outside of the source deployment is to create a group with title = 'ng6_superadmin'. For additional informations, check the SQL file.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/60Merge branch issue#121 with master2019-10-24T09:39:03+02:00Romain ThervilleMerge branch issue#121 with masterThe purge mails 'Errors-To:' field has been set to the 'email_from'
value, instead of 'email_copy'.
Issue#121The purge mails 'Errors-To:' field has been set to the 'email_from'
value, instead of 'email_copy'.
Issue#121V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/61merge branche issue#119 with master2019-10-24T09:50:03+02:00Romain Thervillemerge branche issue#119 with masterUpdate the run and analysis display to add the data state, and retention limit.
commit 20f6a237798424ef1b82cb236ff21fbbaaba03be
issue #119Update the run and analysis display to add the data state, and retention limit.
commit 20f6a237798424ef1b82cb236ff21fbbaaba03be
issue #119V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/58#134 : debug ng6workflow.py and sample.py2019-10-28T10:29:18+01:00Claire Kuchly#134 : debug ng6workflow.py and sample.pyindex files in casava directory who isn't 10X data.index files in casava directory who isn't 10X data.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/59Merge branch issue#126.2 with master2019-10-28T10:29:29+01:00Romain ThervilleMerge branch issue#126.2 with masterSuperadmin users are now allowed to update any user (and their
password), from any project.
issue #126Superadmin users are now allowed to update any user (and their
password), from any project.
issue #126V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/62[demultiplexont.py]2019-10-28T13:22:00+01:00Audrey Gibert[demultiplexont.py]Script was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process partScript was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process partV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/64Merge branch issue#120 with master2019-11-12T13:39:32+01:00Romain ThervilleMerge branch issue#120 with masterfile_put_contents() php logs have been removed.
(Refactoring only commit)
issue #120file_put_contents() php logs have been removed.
(Refactoring only commit)
issue #120V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/63#139 debug2019-11-13T15:25:44+01:00Claire Kuchly#139 debugDebug number of reads add to saved files for illumina ng6 workflow.Debug number of reads add to saved files for illumina ng6 workflow.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/65#141 change REGEX to display pictures from FASTQC analysis from new2019-11-13T15:26:01+01:00Claire Kuchly#141 change REGEX to display pictures from FASTQC analysis from newstorage spacesstorage spacesV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/66Merge branch Issue#129 with master2019-11-19T09:32:54+01:00Romain ThervilleMerge branch Issue#129 with masterV3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/67Merge branch issue#119.2 with master2019-11-21T15:47:34+01:00Romain ThervilleMerge branch issue#119.2 with master- Display fixed when the analysis or run's data state is 'extended'
- New line in the analysis and run single element display, indicating
the purge date when the element has been purged.
issue#119- Display fixed when the analysis or run's data state is 'extended'
- New line in the analysis and run single element display, indicating
the purge date when the element has been purged.
issue#119V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/71Merge branch issue#119 with master2019-11-28T17:37:57+01:00Romain ThervilleMerge branch issue#119 with masterMinor visual update for the retention display in the single run and single analysis views.
issue #119Minor visual update for the retention display in the single run and single analysis views.
issue #119V3.2.6Romain ThervilleRomain Therville