@@ -36,7 +36,7 @@ task batch { | |||
cd /cromwell_root/tmp/cnvkit | |||
mkdir results | |||
cnvkit.py batch -p $nt ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \ | |||
--method ${method} --segment-method ${segment_method} \ | |||
--method ${method} \ | |||
${access_opt} ${annotate_opt} \ | |||
--fasta hg_ref.fa ${reference_opt} \ | |||
--output-reference ${sample_id}.reference.cnn \ |