- Cutadapt: simplify interface
- Bigger memory multiplier in mutect to take in account bigger vmem usage
- Cutadapt: Remove default adapter
- Fastqsplitter: use version 1.1.
- Picard: Use version 2.20.5 of the biocontainer as this includes the R dependency
- Common: Update dockerTag to dockerImage.
- GATK: Add CombineVariants task that allows, e.g., to merge VCFs from different callers.
- Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).
- Mutect2: Add "--germline-resource" and "--f1r2-tar-gz" inputs, requiring an update to GATK 4.1.2.0.
- Mutect2: Add necessary missing index attribute for panel of normals.
- MultiQC: Add memory variable to multiqc task.
- GATK: SplitNCigarReads, BaseRecalibration and ApplyBQSR do no longer need regions files as required inputs.
- VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
- Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
- Cutadapt: Fix issues with read2output when using single-end reads.
- Add feature type, idattr and additional attributes to htseq-count.
- Added allow-contain option to bowtie.
- Added a changelog to keep track of changes.