1.2.3

[maxulysse]

• Test on Bianca
• Sublists of containers are in the containers documentation
• Bug fixed on VEP containers
• Bug fixed with Singularity containers on /scratch - fixes RunHaplotypecaller fails on scratch #471 (runOptions = "--bind /scratch")
• No need for TSV on annotate step - resolves We do not need a tsv file when starting from the annotate step #480
• Sort .gitignore and add *.img
• Move buildContainers.nf test further down
• Default params moved out of nextflow.config to their own scripts
• buildContainers.nf params singularityPublishDir is now containerPath
• new containers.config file to simplify docker.config and singularity.config files
• params.tag is the Docker Hub containers tag
• params.repository is the Docker Hub containers repository
• params.containerPath is the path to the containers (for NGI deployment)
• Documentation updated
• Improve snpEff output
• Improve VEP output
• Improve MultiQC report header
• Improve tests
• Improve skeleton script to launch on /scratch