levim/strelka1 repository overview

#cp out config file
singularity exec strelka1-1.0.15.simg \                
       cp /strelka_workflow-1.0.15/etc/strelka_config_bwa_default.ini [...]/strelka_config_bwa_default.ini;

#make necessary edits to config file
sed -i '13s/.*/isSkipDepthFilters = 1/' [...]/strelka_config_bwa_default.ini;

#configure workflow
singularity exec strelka1-1.0.15.simg \               
       /strelka_workflow-1.0.15/bin/configureStrelkaWorkflow.pl      \
        --normal={input.normal} \
        --tumor={input.tumor}    \          
        --ref={input.ref}                \
        --config=[...]/strelka_config_bwa_default.ini    

#run strelka
singularity exec strelka1-1.0.15.simg \
         make -j {threads};