ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:21:28+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/221[IlluminaWF] Change algo use with BWA for ContaminationSearch analysis2022-12-16T16:21:28+01:00Jules Sabban[IlluminaWF] Change algo use with BWA for ContaminationSearch analysisCurrently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeli...Currently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeline under Nextflow we will use ***FastqScreen*** to make this analysis. This tool already use `bwa mem`.
So to have comparable results between the two pipelines, we must change `bwa aln` to `bwa mem`.Jules SabbanJules Sabbanhttps://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/167[Sequel2] make available BAM format from addrun2022-12-16T16:21:28+01:00Celine Vandecasteele[Sequel2] make available BAM format from addrunCurrently we can only make available fastq format when we add a run in NG6.
Data size on NG6 should be calculated from bam format.
#149Currently we can only make available fastq format when we add a run in NG6.
Data size on NG6 should be calculated from bam format.
#149Audrey GibertAudrey Giberthttps://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/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/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/185Adding a warning to prevent users from lauching 20+ direct url downloads at t...2022-12-16T16:21:28+01:00Romain ThervilleAdding a warning to prevent users from lauching 20+ direct url downloads at the same timeThis morning, the nG6 virtual server had a 40+ load average.
The cause seems to be a big number of direct downloads (urldownload method) from a single user.
We should add a warning like:
"If you need to recover a large number of files, ...This morning, the nG6 virtual server had a 40+ load average.
The cause seems to be a big number of direct downloads (urldownload method) from a single user.
We should add a warning like:
"If you need to recover a large number of files, please copy the links and only launch 2 to 3 downloads at the same time (Either with the wget command, or with your web browser). Thank you."Romain ThervilleRomain Thervillehttps://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/33correct source indent (tabs/white space) for all files2019-08-29T14:11:18+02:00Gerald Salingerald.salin@inra.frcorrect source indent (tabs/white space) for all filesV4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/87Enhancing the display of a project search result2019-08-29T14:24:03+02:00Audrey GibertEnhancing the display of a project search resultI was looking for project Epi on the ng6 project page.
It appears on the 2nd page of search result because according to ng6, space character comes after letters.I was looking for project Epi on the ng6 project page.
It appears on the 2nd page of search result because according to ng6, space character comes after letters.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/108export metadata2019-08-30T09:27:13+02:00Celine Noirotexport metadataadd a functionality to export all metadata of project, run, analysis.add a functionality to export all metadata of project, run, analysis.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/109ftp server architecture2019-08-30T09:27:13+02:00Celine Noirotftp server architectureKeep/generate run/analysis architecture for a project when ftp server will be available.Keep/generate run/analysis architecture for a project when ftp server will be available.V4 - MaintenanceGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/181make filenames in NG6 uniq2020-05-15T07:36:11+02:00Gerald Salingerald.salin@inra.frmake filenames in NG6 uniqin NG6 FAQ, for downloading :
On a Windows workstation (Command lines), copy/paste this list in a file "listOfFiles" (B**e aware that if the same filename is found in different url, the local file will be overriden**). Then you can down...in NG6 FAQ, for downloading :
On a Windows workstation (Command lines), copy/paste this list in a file "listOfFiles" (B**e aware that if the same filename is found in different url, the local file will be overriden**). Then you can download curl for Windows (https://curl.haxx.se/download.html), extract the archive, and run this following command in a windows prompt
should not happen.
prefix the filename so that it is uniq (add the name of the parent folder which is uniq? the run Id + analysis Id?)V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/142manage run 10X with samples with custom index that have to be processed like ...2022-12-16T16:21:27+01:00Claire Kuchlymanage run 10X with samples with custom index that have to be processed like 10X samplesLike SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 1...Like SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 10X illumina qc workflow.Claire KuchlyClaire Kuchlyhttps://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 Gibert2020-09-30