This repo follows the progress of transfering the GenPipes' DNASeq mugqic protocol into WDL to use on cloud infrastructure.
A WDL scheduler has been added to GenPipes on the wdl_scheduler branch
A test environment has been set up on Beluga at:
/home/rdali/projects/rrg-bourqueg-ad/rdali/C3G/projects/dnaseqTestSet
salloc -N 1 -n 1 --mem 10Gb --account=rrg-bourqueg-ad --time=2:00:00
module load mugqic/java
python utils/readset2json.py -r readset.dnaseq.full.txt -n DnaSeq
jq -s '.[0] * .[1]' dnaseq_genpipes.json myReadsetFile.json > dnaseq_genpipes_readset.dnaseq.full.json
java -jar $wdltool validate dnaseq_genpipes.wdl
sbatch --account=rrg-bourqueg-ad --time=24:00:00 -N 1 -n 1 --mem 10G -o slurm.cromwellTest_test --wrap="module load mugqic/java/openjdk-jdk1.8.0_72; java -Dconfig.file=./cromwell.conf -jar $cromwell run dnaseq_genpipes.wdl --inputs dnaseq_genpipes_readset.dnaseq.full.json --options ./options.json"
Where:
wdltool=/home/rdali/tools/womtool-51.jar
cromwell=/home/rdali/tools/cromwell-51.jar