Merge branch 'develop' into release/v2.0.3

UMCUGenetics · Jun 11, 2024 · ccdd0c5 · ccdd0c5
2 parents 2314388 + b70c2f5
commit ccdd0c5
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/WGS.nf b/WGS.nf
@@ -150,7 +150,11 @@ process ExonCov {
     script:
         """
         source ${params.exoncov_path}/venv/bin/activate
-        python ${params.exoncov_path}/ExonCov.py import_bam --threads ${task.cpus} --overwrite --exon_bed ${params.dxtracks_path}/${params.exoncov_bed} ${analysis_id} WGS ${bam_file}
+        flask --app ${params.exoncov_path}/ExonCov import_bam \
+        --threads ${task.cpus} \
+        --overwrite \
+        --exon_bed ${params.dxtracks_path}/${params.exoncov_bed} \
+        ${analysis_id} WGS ${bam_file}
         """
 }