Here is an example config.json:
{
"base": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0",
"data": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/data",
"ref": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/ref",
"src": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/src",
"var": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/var",
"result": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/result",
"run": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/run",
"etc": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/etc",
"logs": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/logs",
"archive": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/archive",
"usr": "/lustre_cfc/ws_qstor/ws/afaaj01-QLBAB_EXOME-0/usr",
"params": {"fasta": "/lustre_cfc/qbic/reference_genomes/Homo_sapiens/DNA/2016.01.21.UCSC/hg19/Sequence/BWAIndex/hg19/hg19"}
}Note that in contrast to the RNA-Seq workflow you do not need a params.json file here.