Small bugfixes

uclahs-cds · Jul 25, 2024 · 5a2745a · 5a2745a
1 parent 8b87584
commit 5a2745a
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/module/sv_workflow.nf b/module/sv_workflow.nf
@@ -20,7 +20,7 @@ process run_sv_liftover{
 
     script:
         """
-        Rscript "${moduleDir}/scripts/liftover-Delly2-vcf.R \
+        Rscript "${moduleDir}/scripts/liftover-Delly2-vcf.R" \
             --input-vcf "${vcf}" \
             --header-contigs "${header_contigs}" \
             --chain-file "${chain_file}" \
@@ -52,7 +52,7 @@ process run_intersect_gnomad {
 
     script:
         """
-        Rscript ${moduleDir}/scripts/publish/extract-vcf-features-SV.R \
+        Rscript ${moduleDir}/scripts/publish/extract-vcf-features-SV.R" \
             --variant-caller "${variant_caller}" \
             --input-vcf "${vcf}" \
             --output-rds "annotations.Rds" \

diff --git a/nftest.yml b/nftest.yml
@@ -3,6 +3,7 @@ global:
   temp_dir: test/work
   remove_temp: true
   clean_logs: true
+  nf_config: test/common.config
 
 cases:
   - name: SNV