Tags

# Improvements
- fastqscreen section multiQC has its tips in blockquote #155
- Aviti fastq headers have been anonymized #156

# New feature:
- Get unmapped reads (from bwa, star and salmon) into fastq files in alignment/unmapped folder #136

# Improvements:
- No more BAM files are stored anymore #154
- Add Help4MultiQC link in mqc report #153
- Add advice to interpret some graphs #152

- Remove GitLab link and getplage.contact eamil in MultiQC #143
- Use sample list in readset creation #144
- Analysis creation waits the end of ngsrg treatment creation at readset level to be executed #145
- Remove useless process configuration in dex mode #148
- Ignore exit status 6 in Analysis Creation #149
- Use new conf of MultiQC # 150
- Remove md5sum generation and file adding to readsets #151
- Add 10X index files to /save/ngl #147

- Support for simple indexes in the Aviti demultiplexStats and the management of undetermined #135
- New function and use of the shared process to create the info header in the MultiQC #137 #139
- Uniqueness of the MultiQC name: projet_pool_flowcell_lane_multiqc.html #138
- Fixed a problem with the empty channel for the illumina demultiplexStat which was no longer inserted #140
- Improvements to the final email: it no longer says that the data is not on ngl while it is there for aviti, and added a link to the analysis if it has been created otherwise to the run # 141

# New feature
- Added the NGSRG treatment at the readset level for elemebio #130

# Improvements
- Added the name of the analysis (the run_name of jflow for illumina, the run_name of the YAML for aviti) #134
- Fixed an error display bug when sucess at the end of the pipeline
- Created the Map of emails at the beginning of the pipeline to match the changes of shared_modules #132
- Complete removal of the name of the technology in the conf #133

# Improvements
- Modification of default email adress for labo and bioinfo #127
- Update NGL-Bi URL in email template #128
- Limit execution of NGSRG readset treatment to illumina 

# New feature
- Some modifications to reuse scripts and modules to create demultiplexStats treatments (lanes/readsets) on aviti data #126

# New feature
Add creation of illumina NGSRG treatment at readset level #125

Bug fixed 
- fastq adding to readset step is now done once, not more #123

# New features
- Insert nextflow launchDir and resultDir in Analysis properties # 122
- Use of shared groovy functions  and creatation of new ones #50
- New template for error email #50
- New parameter for NGL project hash with no default value: `project_hash` #50

# Improvements
- Autobuilding of the output directory path #120
- Remove unused few parameters #50

# Bugs fixed
- nextflow main config file can now get number of samples on the lane #119
- The DTM_mode parameter is now well evaluated #118

# Improvements
- Change name of pipeline (in several email fields) to 'short reads' instead of 'illumina' #114
- Group (almost) every NGL related process to a unique subworkflow #117

# New feature
- Use the shared_module's subworkflow to create Analysis, store files and update state #111 and #117 

# Bugs fixed
- Elembio demultiplexStats script get the correct sequences count and make itself the percOfFrag values #112
- Illumina demultiplexStats script does not get the bcPerfect barcodes count for allOther indexes anymore #115
- Channels versions of some process in module_dna can now be retrieve #116
- The ressource factor can no longer be smaller than 1 #113

# New features
- Automatic closing of NGL-SQ Experiement #104
- Get software version and display them in the MultiQC report #15
- Get and export existing readset codes in case of resume pipeline #108
- Update the MultiQC version to 1.24.1 #15
- New ext.args for DUPLICATED_READS process

# Improvements
- Acceleration of sortemerna execution #109
- Export log files of TREATMENT_DEMUX processes #110
- Remove useless CI/CD files

# 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

# 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

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

# 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

Hot fix to get ngl-biRunCode from file

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

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