Tags give the ability to mark specific points in history as being important
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V1.31.0
f0689249 · ·# New feature - Undetermined files are now include in QC sub-workflow and added to NGL-Bi::Analysis. Enabled by new parameter: --with_undetermined #177 # Improvement - Show percentages instead of number for methylated cytosines in multiQC #178
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V1.30.0
a3b0d6be · ·# Improvements & new feature - Store genome/transcriptome reference fasta and index files into Channels. Create index if needed for every aligner #131 - Single end fastq files can be analyzed #43 - Improve qualimap resource allocation # Bug fixed - Validation of reads structure after subsampling (with pair end assocation checking if needed) #146
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V1.29.3
03312360 · ·# Improvements - Reference genome for EMSeq subworflow is not mandatory anymore #171 - Only one mail is sent at start #172
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V1.29.0
e4069d7b · ·New features - parameter management and validation were converted from custom groovy to nf-schema pluggin #168 - Add validation for some params which depend on another (not available with nf pluggin) - Add documentation files about JSON-schema, nf-pluggin and pipeline parameters - New subworkflow for EM-Seq analysis Improvements - The nextflow workdir is not keep anymore for aviti runs #167 - Little modification on RNA data nature detection
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v1.29.0
e4069d7b · ·New features - parameter management and validation were converted from custom groovy to nf-schema pluggin #168 - Add validation for some params which depend on another (not available with nf pluggin) - Add documentation files about JSON-schema, nf-pluggin and pipeline parameters - New subworkflow for EM-Seq analysis Improvements - The nextflow workdir is not keep anymore for aviti runs #167 - Little modification on RNA data nature detection
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V1.28.0
adb200cd · ·## Improvements & new features - Stop keeping non-rRNA fastq files, to save disk space #158 - Remove poolName option for RS creation #160 - Use qualimap and samtools versions in mqc #157 - Final email warns if pipeline was resumed #161 - Prevent white space when using params.run_name everywhere #164 - Merge of R1 and R2 sample names in Multiqc (update of mqc version) #162 #163 - Uniformization of mqc modules names. ModuleName - Tool/Context #163 - Fix ymax value to 100 for N content and adapter fastqc plots - Remove fastqc_overrepresented_sequences and fastqc_status_checks graphs from mqc ## Bug fixed - Stop modify fastq headers for AVITI #159
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V1.27.6
f10db1fd · ·# Improvements - fastqscreen section multiQC has its tips in blockquote #155 - Aviti fastq headers have been anonymized #156
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V1.27.4
332903e5 · ·# 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
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V1.27.0
ca4b7700 · ·- 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
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V1.26.5
be16cee3 · ·- 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
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V1.26.0
5282ed34 · ·# 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
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V1.25.3
b787e4fe · ·# 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
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V1.25.0
9cd7b92a · ·# 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
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V1.24.0
67168dc8 · ·# 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
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V1.23.0
40e958f4 · ·# 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