GitLab

Bug fix:

• The switch_space_id workflow now updates the paths to the moved analysis result files. issue #129

Bug fixes:

• The file search engine in the addanalysis form has been fixed. Issue #171
• The run button in the addanalysis form now works as intended. Issue #175
• When creating a project, the space id field is now built as a dynamic select field. Issue #172
• The date sorting has been fixed in the run tables. Issue #138

Bug fixes and minor enhancements :

• The project count on the project list has been fixed for user having "member" rights on a hidden project. Issue #154
• The broken links to the project pages in the admin sections "Mail obsolete project" and "Process mail demands" have been fixed. Issue #163
• The hard coded links in "Admin > Extend Project" are now made dynamicaly. Issue #146
• The workflow that creates projects has been fixed. Issue #157
• The "delete_analysis", "add_user" and "delete_purge_data" AJAX calls have been fixed. Issue #171

Visual updates :

• The old static retention period displayed in the purge mails has been removed to avoid inconsistencies. Issue #137
• New column "project space" in the "Process mail demands" admin section. Issue #161
• New space specific retention warning label in application.properties, replacing the expiration limit warning with an explanation on the retention policy. Issue #161
• In the FAQ section, a question has been added and a question has been updated. Issue #161

New features :

• A new purge warning mail template has been made for project belonging to spaces that do not explicitly allow retention extentions (We removed the "Reach us to extend..." part in this new template). Issue #161
• A new "Send mail without extension" button has been added to send the new format. Issue #161
• New search filters in the "Process mail demands" admin section, on "project space" and "delay exceeded". Issue #161

2 features have been updated:

• The "switch_space_id" workflow form (in the single project view) has been made accessible to the current project's administrators. An additionnal step has been added, and we ask for a Genologin (SSH) user+pwd with the rights to write files in the space's data dir. Only ng6, root and users in the apache group can pass this test. So, basicly, this feature now requires the ng6 user credentials. (issue #129)
• The "Administration > Mail Obsolete Project" page has been updated. The table filter on "size" has been replaced by a filter on "space_id".

Several feature and visual fixes for ng6:

• The "download_symlink" workflow has been reworked to allow the download of project data, even if some analysis data folder (Ont_Demultiplex) are empty or missing. This should resolve the CLIMARES download problem. (issue #153)
• The switch_space_id workflow has been updated, to support the migration of missing or empty analyzes. This should resolve the CfDaily problem. (issue #129).
• Update to the "illumina_10X" to handle indexes after illuminafilter. (issue #143)
• A warning is now handled when creating a project (issue #155).
• Several design updates and adjustments (issues #156, #150).

New 'switch_space_id' workflow

• New name : switch_space_id.
• The given space id is checked in application.properties.
• Most of the treatments have been moved to a "components" folder, allowing us to create easily a new "migrate_several_projects" (or "bulk_project_migration") later.
• The workflow can be launched from the single project view on the nG6 website, when logged a superadmin user.
• The project's space_id is visible to everyone on the single project view.
• A warning indicating that the migration updates the retention has been added to the workflow's form in single project view.
• More logs in ng6.log, and the new log file MoveProject.stdout. (path exemple : [...]/jflow/work/switchspaceid/wf000452/MoveProject_default/MoveProject.stdout)
• CSS updates for the project views.
• For new space_ids, the <space_id>/run and <space_id>/analyze directories will be created if missing.

Updates since the last release:

Issue #121 : When sending a purge mail, the "Error-to" mail field will be set as the "email_from" value instead of "email_copy".

Issue #119 : The Run and Analysis views have been updated to include a new line explainig the retention policy.

Issue #126 : The superadmin users can now update any password, and can see all runs on the runs list page. (https://ng6.toulouse.inra.fr/index.php?id=56)

Issue #134 : The "index" variables have been renamed to "readsi". The "index" variable will no longer be overwritten, and the 'Nonetype' error should not appear anymore for 10x runs with indexes.

Issues #131 , #132 , #112 : Pdf files added to analysis for nanopore runs. AligmentStats -> Duplicate output corrected. New analysis : Demultiplex Stat for ONT.

• The branch #126 was missing from the last tag, adding a new superadmin group. (issue#126)
• The workflow 'switch_project_space_id' has been refactored. (issue#129)
• The addanalysis workflow (from command lines AND web interface) has been fixe via an update to jflow.min.js. (issue#95, #85)
• Bug in project view fixed (issue#120)

Same as V3.2.5.3 ( https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/tags/V3.2.5.3 ), with an additional merge:

Adds a new illumuna_qc_10X pipelines to ng6

This tag contains new features and bug fixes:

• New superadmin group

A new superadmin section can be found in Administration > Admin management, only visible to superadmins. Users that belong to this group can acess every project, run and analysis.

• Workflow switch_project_space_id

This new workflow allows to migrate a project to another space_id, defined in application.properties. The project's runs and analyzes are also updated, their files are moved and their retentions are updated according to the configuration file.

• Purge mail reworks

The purge mail will now be sent to every admin, manager and member linked to the project. There is also a new "email_to_discard" parameter in the typo3 template, to remove email adresses from the recipient list.

• Hidden runs and analyzes in project view

The hidden runs and analyzes will not be counted in the project view if they are not visible to the current user.

• '0' character in run names

The character '0' in run names will no longer be normalized as '_' when creating a unix file path.

Contains fixes for the 3.2.5.1 version.

ONT : supress N50 from template, add useful bases and reads, enhancement of ui
AddRawFiles : correct a bug where the counting of reads and bases is done too early, before the presence of all .count files

ng6 with slurm optimization of some data processing for a better efficiency (work on a data subset, parallelization...)

• update jflow version
• less duplication of data for illumina pipelines
• upgrade typo3 plugin to be compatible with the last LTR typo3 version V8 and php 7
• add project and data management, allowing to delete data old data (based on retention date)

Passage de ng6 à Git Intégration de ONT_qc Intégration de la gestion des purges Password updatable