Tags

New features and Improvements
- Update bwa version in fastqScreen conf file
- Improve ressources for fastQC, Sortmerna, Qualimap, 
- Change defaut path to shared_modules, stored on genobioinfo
- Run Qualimap in the RNA pipeline
- DTM mode force to keep the workdir

Bug fixed
- GC_DROPOUT value is now got from report in DTM mode

Merges requests : !11, !12, !13, !14

New features & improvements :
- STAR's logs are now kept #80
- Merge of fastq files by lanes for AVITI data #79
- Keep the wordir if DTM mode is activated #81
- New function to manage requested ressources #84

Bug fixed :
- New default value for the lane in Treatment_demux_run (because of changes in shared_modules) #83

New features & improvement
- New config for NGL-Bi related shared_modules #78
- Add GC bias analysis process in DTM mode (performe analysis and export results in the CSV) #76
- Multipool analysis per lane is now possible (based on multiline jFlow file) #75

Bug fixed
- New config for dev mode #77
- Remove NA in demultiplexStat for MiSeq analysis #73

New features and improvements :
- Add diversity QC subworkflow for 16s/amplicon dataset #71
- Writing of docs/usage.md #74
- Increase memory for seqtk sample process #72

Bug fixed :
- Replace Nas by 0 in demultiplexStat #73

merge request : !8
Milestone : 6

Split CORE pipeline in two.  
The first is especially made for data from bcl2fastq.  
The second can be ran on every fastq files.

Little improvements from V1.2.0

Merge : !2

The pipeline is now ready for DNA and RTL data, if the jFlow file contains only one line.
Other condition is : one project on the lane.
These limitations will remove soon

# New features
- Add scripts for DTM
- Change trim sample method in the MultiQC config file
- Add fastq subsetting step in the CORE pipeline
- Add email sending steps 
- Change params case
and more...