ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-02-11T17:17:45+01:00https://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/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/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/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/63overriding batch_option values possible?2018-08-14T15:44:30+02:00Gerald Salingerald.salin@inra.froverriding batch_option values possible?to configure time according to the sequencer (or the number of reads?)to configure time according to the sequencer (or the number of reads?)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/55cutadapt output changed from 1.3 to 18 and 1.142018-08-13T19:10:53+02:00Gerald Salingerald.salin@inra.frcutadapt output changed from 1.3 to 18 and 1.14cutadpat component post-proccess failed :
the output no longer contains "Processed reads"
with cutadapt V1.3
`cutadapt version 1.3
Command line parameters: -b CTGTCTCTT -b ATACACATCT -b AGATCTAT -b AAGAGACAG --error-rate 0.1 --minimum-l...cutadpat component post-proccess failed :
the output no longer contains "Processed reads"
with cutadapt V1.3
`cutadapt version 1.3
Command line parameters: -b CTGTCTCTT -b ATACACATCT -b AGATCTAT -b AAGAGACAG --error-rate 0.1 --minimum-length 20 --times 4 --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq -o /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_cut.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_tmp.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_tmp.fastq
Maximum error rate: 10.00%
No. of adapters: 4
Processed reads: 4344
Processed bases: 434400 bp (0.4 Mbp)
Trimmed reads: 2106 (48.5%)
Trimmed bases: 113988 bp (0.1 Mbp) (26.24% of total)
Too short reads: 377 (8.7% of processed reads)
Too long reads: 0 (0.0% of processed reads)
Total time: 0.28 s
Time per read: 0.064 ms
`
with cutadapt 18. and 1.14 :
`This is cutadapt 1.8.3 with Python 2.7.2
Command line parameters: -b CTGTCTCTT -b ATACACATCT -b AGATCTAT -b AAGAGACAG --error-rate 0.1 --minimum-length 20 --times 4 --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq -o /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_cut.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_tmp.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_tmp.fastq
Trimming 4 adapters with at most 10.0% errors in paired-end legacy mode ...
Finished in 0.18 s (41 us/read; 1.45 M reads/minute).
=== Summary ===
Total read pairs processed: 4,344
Read 1 with adapter: 3,610 (83.1%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 377 (8.7%)
Pairs written (passing filters): 3,967 (91.3%)
Total basepairs processed: 814,063 bp
Read 1: 434,400 bp
Read 2: 379,663 bp
Total written (filtered): 686,031 bp (84.3%)
Read 1: 342,864 bp
Read 2: 343,167 bp
`V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/52unable to use the modules functionality of jflow for insertsizes.py component2018-08-13T10:57:08+02:00Gerald Salingerald.salin@inra.frunable to use the modules functionality of jflow for insertsizes.py componentthe process of this module call a self.add_python_execution(inserts_metrics...)
the modules specified in application.properties for InsertSizes component is not managed in jflow as it is a PythonFunction
for the moment we have to put th...the process of this module call a self.add_python_execution(inserts_metrics...)
the modules specified in application.properties for InsertSizes component is not managed in jflow as it is a PythonFunction
for the moment we have to put this module load (module load system/R-3.4.3) in the bashrc fileV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/46weaver : make patch for function.py2019-08-30T09:23:58+02:00Celine Noirotweaver : make patch for function.pyTODO
l214TODO
l214V4 - MaintenanceCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/37Update documentation with rules and modules2018-09-07T12:03:51+02:00Celine NoirotUpdate documentation with rules and modulesBy upgrading jflow, new functionnalities have been added.
The documentation should also be upgrade.By upgrading jflow, new functionnalities have been added.
The documentation should also be upgrade.V4 - 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/32add manual for purging data2018-08-02T14:57:31+02:00Gerald Salingerald.salin@inra.fradd manual for purging dataV4 - MaintenanceClaire KuchlyClaire Kuchly