Fix chromsmask rule

snakecnv/referencebundle.snk

@@ -146,12 +146,13 @@ rule chromsvmask:
     output:
         SUBDIR + "work/svmask_{chrom}.fasta"
     params:
-        rl = config['read_len']
+        rl = config['read_len'],
+        subdir = SUBDIR
     log:
         "logs/svmask/{chrom}.log"
     shell:
         "java -cp {CLASSPATH} -Xmx4g org.broadinstitute.sv.apps.ComputeGenomeMask "
-        "  -R {input.fa} -O work/svmask_{wildcards.chrom}.fasta -readLength {params.rl}"
+        "  -R {input.fa} -O {params.subdir}/work/svmask_{wildcards.chrom}.fasta -readLength {params.rl}"
         " -sequence {wildcards.chrom} 2> {log} "
 
 rule bed2fasta: