ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:21:27+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/230[contaminationSearch] Bwa mem configuration causes some misunderstandings in ...2022-12-16T16:21:27+01:00Claire Kuchly[contaminationSearch] Bwa mem configuration causes some misunderstandings in the calculation of the contamination and explodes the CPU quotat of ng6After several month of bwa meme use for calculation of contamination rate, it appears several problems :
- the calcul of contamination rate is not adapted for what we want to see.
- after a run of NovaSeq we see an large increase of ng...After several month of bwa meme use for calculation of contamination rate, it appears several problems :
- the calcul of contamination rate is not adapted for what we want to see.
- after a run of NovaSeq we see an large increase of ng6 cPU quota due to the parameters used for launched bwa mem analyzis.Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/164[Hi-C] Hi-C pipeline developpement2022-12-16T16:21:28+01:00Claire Kuchly[Hi-C] Hi-C pipeline developpementImplementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer re...Implementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer result (file inter.txt) interface with smartyClaire KuchlyClaire Kuchly2020-04-30https://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/91[methylseq] do not store files for analyses Alignment and Metylation extractor2018-11-06T17:50:17+01:00Gerald Salingerald.salin@inra.fr[methylseq] do not store files for analyses Alignment and Metylation extractorthese data are too huge and for no use after the quality pipeline is overthese data are too huge and for no use after the quality pipeline is overV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/165[Nanopore] Add "metadata_fast5.txt" in logs file on NG62020-02-06T14:12:27+01:00Roxane Boyer[Nanopore] Add "metadata_fast5.txt" in logs file on NG6See issue 45 from NGS_ONT project to find more.See issue 45 from NGS_ONT project to find more.https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/173[Nanopore] Add graph for each sample on multiplex run2020-03-03T13:41:40+01:00Claire Kuchly[Nanopore] Add graph for each sample on multiplex runhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/94[ont_qc] ne pas mettre en dur la compression2019-02-11T17:17:45+01:00Gerald Salingerald.salin@inra.fr[ont_qc] ne pas mettre en dur la compressionself.compression = "gz" dans la fonction process de __init__ du pipelineself.compression = "gz" dans la fonction process de __init__ du pipelinehttps://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/92AddRawFilesComponent is not displayed on ng6 interface2018-11-08T17:18:58+01:00Audrey GibertAddRawFilesComponent is not displayed on ng6 interface![image](/uploads/ddcac4b0e5f54501039d0cd6b28e5daf/image.png)![image](/uploads/ddcac4b0e5f54501039d0cd6b28e5daf/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/187An update to analysis.py has introduced a bug and stopped to workflows in pro...2022-12-16T16:21:27+01:00Romain ThervilleAn update to analysis.py has introduced a bug and stopped to workflows in progressThe commit eb9dd0cb292d57be2c1ec9f74e9e54d94d4e2bed (issue #129) has introduced the following error:
Traceback (most recent call last):
File "/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w000069...The commit eb9dd0cb292d57be2c1ec9f74e9e54d94d4e2bed (issue #129) has introduced the following error:
Traceback (most recent call last):
File "/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w0000699", line 92, in <module>
outputs = add_analysis(*new_args)
File "/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w0000699", line 73, in add_analysis
analysis.post_process()
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.2/src/weaver/../../workflows/components/fastqc.py", line 124, in post_process
job 32605 completed
/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w0000742 none /work/ng6/jflow/work/illumina_diversity_qc/wf006442/Flash_default/analysis.cfg /work/ng6/jflow/tmp/tmp29fg5x0m.dump /work/ng6/jflow/work/illumina_diversity_qc/wf006442/FastqIlluminaFilter_default/analysis.cfg failed with exit code 1
sample + ".per_tile_quality.png"), "ptqpng")
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.2/src/weaver/../ng6/analysis.py", line 625, in _save_file
return self.get_web_filepath(file_name, 'fileadmin')
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.2/src/weaver/../ng6/analysis.py", line 774, in get_web_filepath
return base_filepath + os.path.join(self.get_directory(), file_name)
File "/tools/python/3.4.3/lib/python3.4/posixpath.py", line 82, in join
path += b
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'str'
For the time being, I've rolled back to a previous version.
Problem : To test the build, I've used a simple addanalysis. It wasn't enough.
The tests in issue #152 should cover more user cases, they are currently to weak.
A big shell script to test everything at once would be great.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/180Analysis sort by data in project view2020-05-05T14:40:13+02:00Celine NoirotAnalysis sort by data in project viewUnable to sort project analysis by date
![image](/uploads/f37bbc5558f1d7655864dd3a3ef086cb/image.png)Unable to sort project analysis by date
![image](/uploads/f37bbc5558f1d7655864dd3a3ef086cb/image.png)V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/162Change the way the number of reads and the base pair for run information are ...2022-12-16T16:21:27+01:00Claire KuchlyChange the way the number of reads and the base pair for run information are calculated in the 10X analysisThe number of reads and base pair are calculed in all fileS ( R1, R2, I) or we want to have just the R1 and R2 informations.The number of reads and base pair are calculed in all fileS ( R1, R2, I) or we want to have just the R1 and R2 informations.Claire KuchlyClaire Kuchly2020-02-29https://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/83copy to clipboard from download windows does not work2020-06-11T17:09:25+02:00Gerald Salingerald.salin@inra.frcopy to clipboard from download windows does not work![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe w...![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe we have to upgrade the ZeroClipBoard.min.js file (3 yers old)Romain ThervilleRomain Thervillehttps://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 Therville