wdl based hts-analysis for slurm cluster with enviroment modules.
- is to get generic alignment working.
- basic variant calling (haplotypecallerGvcf).
- somatic variant calling(MuTect2,...).
- ichorCNA integration.
- Variant annotation
- Functional filtering of vcfs
- Stability over > 10 samples
- Rework dir structure to be more in line with warp/other public resources
- End to end easybuild install
Relevant example resources for writing wdl files :
Run the cromwell validation tool womtool to validate the input and generate a template input file. for sampleJson see ./tests/data/raw/fastq/samples.json. See below for the most simple run example
java -Xmx8g -Dconfig.file=./path/to/cromwell.conf -jar ./path/to/cromwell.jar run Bestie.wdl -i inputs_integration.json
easybuild the required modules or use future wrapper module