rdali / dnaseq_wdl

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dnaseq_wdl

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

Tests on Beluga:

A test environment has been set up on Beluga at:
/home/rdali/projects/rrg-bourqueg-ad/rdali/C3G/projects/dnaseqTestSet

need interactive node to run Java on Beluga:

salloc -N 1 -n 1 --mem 10Gb --account=rrg-bourqueg-ad --time=2:00:00
module load mugqic/java

make json input from GenPipes readset file:

python utils/readset2json.py -r readset.dnaseq.full.txt -n DnaSeq

merge the parameter json with the readset json:

jq -s '.[0] * .[1]' dnaseq_genpipes.json myReadsetFile.json > dnaseq_genpipes_readset.dnaseq.full.json

validate wdl script:

java -jar $wdltool validate dnaseq_genpipes.wdl

run command through SLURM:

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

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