Tags

V1.20.0

# New feature
- New subworkflows and process for Element's data (demultiplexStat, remove merge_lanes process, use lane number to get fastq files, ...) #96

# Improvements
- FastqScreen config file in the assets folder is use by default if no one is in the demultiplexed data folder #105
- Workflow's names have been changed : QC_ANALYSIS -> PLAGE, ILLUMINA_QC -> SHORT_READS_QC #106
- Illumina related NGL-Bi process have been moved into CORE_ILLUMINA sub-workflow #107
- MD5SUM process are called with the extension of file to run on

V1.19.0

# New feature and improvement
- Add direct link to NGL-Bi in final email #103
- Add the MultiQC report to the NGL-Bi Analysis #101
- Add 10X subworflow with file management #5

# Bug fixed
- Fastq channel now get each file once #100

V1.18.0

# Improvement and new features
- Replace local begin_nglbi subworkflow by its in shared_modules #97
- Add NGL-Bi Analysis creation  #98

V1.17.0

# New feature 
    - Add NGL-SQ Experiement Code and NGL-Bi Run Code in emails and MultiQC

# Bug fixed 
    - Qualimap reconization memory in case of decimal value
    - Little error when NGL-Bi run is created again in nextflow

V1.16.1

Hot fix to get ngl-biRunCode from file

V1.16.0

Improvements and New features :
- Update sortMeRNA databases #85
- Add Qualimap to the RNA pipeline #88
- New way to rename files before adding them in NGL-Bi (with sequence index) #91

Bugs fixed :
- Add R dependency for picard's process #86
- Correct the column gotten to find the GC_DROPOUT value #87

V1.15.0

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

V1.14.0

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

V1.10.0

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

V1.8.0

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

V1.6.0

merge request : !8
Milestone : 6

V1.4.0

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

V1.3.0

V1.2.4

Little improvements from V1.2.0

V1.2.0

V1.0.0

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...