TOGGLE Logo

Toolbox for generic NGS analyses

  1. Release 0.3.6, 22nd of february, 2018
  2. Release 0.3.5, 8th of November, 2017
  3. Release 0.3.4, 27th of September, 2017
  4. Release 0.3.3, 5th of April, 2017
  5. Release 0.3.2, 1st of March, 2017
  6. Release 0.3.1, 11th of January, 2017
  7. Release 0.3, 16th of March, 2016
  8. Release 0.2.1, 15th of May, 2015
  9. Release 0.2, 14th of March, 2015

Release 0.3.6, 22nd of February, 2018

Functions

Modules

  • Nothing new

Various

  • Linear mode is now launch through scripts, as for scheduler mode
  • Update of the installation script
  • Update of licences
  • Various debugging

Release 0.3.5, 8th of November, 2017

Functions

Modules

  • including the possibility of transferring data using scp command by adding $scp tag in the configuration file More details in Manual

Various

  • Diverse bugs corrected

Release 0.3.4, 25th of October, 2017

Functions

  • New version of scheduling system, including the possibility of adding bash commands with the $env key More details in Manual
  • Adding check format fasta for the reference file.

Modules

  • Adding BWA-SW
  • Adding NGSUtils - bamutils

Various

  • Update DevManual
  • Diverse bugs corrected

Release 0.3.3, 5th of April, 2017

Functions

  • New possibilities for QC: checkFormat for FASTA, FASTQ, SAM/BAM and VCF.
  • Software versions checked before launching (tracability).
  • Current TOGGLE version checked before launching.
  • Adding fastqUtils internal tools : checkEncodeByASCIIcontrol (64 or 33 PHRED format control).
  • Adding blocks for samToolsDepth, samToolsFaidx, samToolsIdxstats, samToolsMerge.

Modules

  • Adding checkFormat.pm

Various

  • Diverse bugs corrected

Release 0.3.2, 1st of March, 2017

Functions

  • In the Global log file print only path and version of softwares used in the workflow

Various

  • Syntax errors corrected in TOGGLEinstall.pl
  • Diverse bugs corrected

Release 0.3.1, 11th of January, 2017

Functions

  • Adding the MPRUN and LSF Scheduling system (through bash script launching)
  • Adding the possibility to add ENV variables
  • Some options are not required anymore
  • Users can by pass the FASTQ checking in order to accelerate launching
  • Help has been optimized (-h options)

Modules

  • Adding tgicl
  • Adding Trinity
  • Adding samtools MpileUp
  • Adding snpEff annotation

Various

Divers bugs corrected

Release 0.3, 16th of March, 2016

Modules

  • Adding the picardTools AddOrReplaceReadGroup CleanSam ValidateSamFile SamFormatConverter
  • Adding the GATK UnifiedGenotyper BaseRecalibrator PrintReads
  • Adding the samTools sortSam flagstats depth idxstats
  • Adding scheduler.pm module for scheduling system
  • Adding the SGE and Slurm schedulers
  • Adding cleaning and compression of given steps

Functions

  • On the fly creation of pipeline (see MANUAL.md for a detailled explanation)
  • Use of Graphviz to generate a visual output of the pipeline structure
  • Adding the automatic scheduling-aware launching system - For SGE and Slurm
  • Adding a cleaning and a compression system to remove/compress chosen intermediate data in order to save hard drive space (see MANUAL.md)
  • Use of initial compressed gzipped files
  • Possibility of starting from FASTQ, SAM/BAM or VCF (gzipped or not)
  • Possibility of working in relative path
  • Providing an output folder in order to not modify the input data (working with symbolic links)
  • Single creation of index/dictionary for reference, once per pipeline and no more once per sample, only if they do not exist.

Release 0.2.1, 15th of May, 2015

Addition to previous version

  • Adding correct SGE version for globalAnalysis.pl
  • Adding RNAseq pipeline v1

Corrections of bugs

  • Correction of the ls bug for only a single pair
  • Correction of hard coded path
  • Validation of current softwares versions
  • Modification of the FASTQ format control
  • Various minor bugs adjustments

Software versions tested

  • bwa
  • Picard-tools 1.124 and Higher
  • SAMtools
  • GATK
  • FastQC
  • CutAdapt
  • Java

Release 0.2, 14th of March, 2015

Second version release