version 0.5.2.0

new evolution of the HiC processing pipeline (hicup + fithic)

version 0.5.1

HiC pipeline refactored and improved using:

• HiCup for mapping and artefact assessment
• HiCorrector for bias correction of the contact matrix
• Fit-hi-c with fixed size bins for significance assessment
• TADbit for calling topological domains

Hiclib support has been discontinued.

version 0.5.0

v0.5.0

version 0.5.0

version 0.4.0 patch 2

Bugfixes in:

• MEME pipeline and reporting.
• Report generation for fastqscreen v 0.4.2

Enhancements:

• TRIMGALORE default resource allocation adjusted
• Bam index generation for Bowtie1 mapping
• Report generation for fastqc paired-end libraries

version 0.4.0 patch 1

Bugfixes in:

• smoketest
• hiclib pipeline
• hicup pipeline
• homer chipseq pipeline

Enhancements:

• gatk pipeline (compatibility to v2.8.1)
• homer Chipseq (input library processing)

version 0.4.0

see Changelog

version 0.3.0

• New debug-mode (executes locally; display logs in terminal)
• Changed direct-mode (executes locally; saves logs as in armed)
• Support for Tophat2.0.10
• Setup script to support install
• Sample pattern parsing for input files
• HTSEQCOUNT extended
• Wiggler extended
• List of references added to report
• FastQC mod standardised
• Default mod configuration refactored
• Index generation for mapping refactored into separate mods
• TASK variable names refactored for consistency

version 0.2.0 patch 1

Bugfix: detecting already processed files
Bugfix: recovery mode in pipelines
Bugfix: detecting fastq-encoding
Bugfix: enable single-end library in Bam2BW conversion

Recovery Enabled Pipeline

• New trigger modes (recover, new data sets)
• Redesigned Project Cards summary report
• Job chaining / Pipeline
• Smoketests
• New modules (trinity, ChIPseq, variant calling, RNAseq, Blue, MEME,...)
• Bugfixes