0.3.8

Various

• Data test directory has been transfered on a external server
• Allowing use a BAM list instead of single BAM file at samtoolsDephtBlock.txt and samtoolsMergeBlock.txt
• Available downloadTest.sh script to download data test

Modules

• Minor bug was fixed in naming variable at addingNewSoft.pl script
• Minor bug was fixed in naming variable "bamFile" at HTseq.md module
• Bug was fixed to correctly copy data when final step output was in NA mode at onTheFly.pm module

0.3.7

Functions

• New softwares:

  • Stringtie
  • HiSat2
  • Nanoplot
  • GENERIC function, allowing to add any function not already installed in TOGGLe (!! EXPERIMENTAL !!), see the manual

• New functions:

  • Possibility of adding samples on an already run job w/o re-running everythin (-add/--add option)
  • Possibility of rerunning a workflow previously stopped because of different problems (-rerun/--rerun option)

Modules

• Reforging the code for easier adding of new software, with the addingNewSoft.pl script

Various

• Correction of an error linked to SGE when the readgroup starts by a number
• Correction of the copy of the true final step in the finalResults folder
• More explicit logs
• Various debugging

0.3.6

Functions

• New softwares:
  • BEDtools
  • Abyss
  • BreakDancer
  • Pindel
  • SNiPlay tools
  • eaUtils
  • checkFormat for GFF and BED
• PDF reports generated through the -report option

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

0.3.5

Functions

• New softwares:
  • Crac
  • Bowtie
  • Bowtie2
  • Atropos
  • DuplicationDetector

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

0.3.4

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

0.3.3

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

0.3.2

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

0.3.1

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

TOGGLEv0.3.0

First official release of the onTheFly version of TOGGLE, allowing the on the fly creation of pipelines.

TOGGLEv0.2.1

Last release version with old fashioned TOGGLE.
This version is the one from the Monat et al., 2015, BMC Bioinformatics original paper, with correctd bugs