diff --git a/etc/settings.yaml.in b/etc/settings.yaml.in index 9d6ef6d..1757d70 100644 --- a/etc/settings.yaml.in +++ b/etc/settings.yaml.in @@ -14,6 +14,7 @@ execution: stack: 128M queue: all contact-email: none + args: '' rules: __default__: threads: 1 diff --git a/pigx-rnaseq.in b/pigx-rnaseq.in index a137d7e..95e8dc6 100644 --- a/pigx-rnaseq.in +++ b/pigx-rnaseq.in @@ -330,6 +330,8 @@ if config['execution']['submit-to-cluster']: else: raise qsub = "qsub -V -l h_stack={cluster.h_stack} -l h_vmem={cluster.MEM} %s -b y -pe smp {cluster.nthreads} -cwd" % contact_email_string + if config['execution']['cluster']['args']: + qsub += " " + config['execution']['cluster']['args'] command += [ "--cluster-config={}".format(cluster_config_file), "--cluster={}".format(qsub),