test workflow

tasks/fastq_ncm.wdl

@@ -13,7 +13,7 @@ task fastq_ncm {
     set -e
     nt=$(nproc)
     export NCM_HOME=/opt/NGSCheckMate
-    python /opt/NGSCheckMate/ngscheckmate_fastq -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf
+    /opt/NGSCheckMate/ngscheckmate_fastq -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf
   >>>
 
   runtime {