diff --git a/snakecnv/tools/pindel.snk b/snakecnv/tools/pindel.snk index 5cd5a36ae665c2240ae4d4e2ac3e64b175256881..269432c0350af89540c0ac1b39a5e24b7384d6a5 100644 --- a/snakecnv/tools/pindel.snk +++ b/snakecnv/tools/pindel.snk @@ -45,7 +45,7 @@ rule pindel: " --number_of_threads {threads}" " --report_interchromosomal_events false" " --minimum_support_for_event 3 -c {wildcards.chrom}:{wildcards.chrbatch}" - " -o {wildcards.batch}/pindel/{wildcard.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}" + " -o {wildcards.batch}/pindel/{wildcards.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}" " 1>{log.stdout} 2>{log.stderr}" """ for svtype in D TD INV RP SI LI BP CloseEndMapped INT_final;