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genomic-medicine-sweden · Oct 10, 2024 · 64c0206 · 64c0206
1 parent 420b8b3
commit 64c0206
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/modules/local/drop_config_runAE.nf b/modules/local/drop_config_runAE.nf
@@ -60,7 +60,7 @@ process DROP_CONFIG_RUN_AE {
 
     snakemake aberrantExpression --cores ${task.cpus} --rerun-triggers mtime $args
 
-    if [[ !skip_export_counts_drop ]]; then
+    if [[ $skip_export_counts_drop == false ]]; then
         snakemake exportCounts --cores 1
         mkdir -p exported_counts
         cp sample_annotation.tsv exported_counts/.
@@ -83,7 +83,7 @@ process DROP_CONFIG_RUN_AE {
     touch OUTRIDER_results_all.Rds
     touch gene_name_mapping_.tsv
     mkdir output
-    if [[ !skip_export_counts_drop ]]; then
+    if [[ $skip_export_counts_drop == false ]]; then
         mkdir exported_counts
     fi
 

diff --git a/modules/local/drop_config_runAS.nf b/modules/local/drop_config_runAS.nf
@@ -57,7 +57,7 @@ process DROP_CONFIG_RUN_AS {
 
     snakemake aberrantSplicing --cores ${task.cpus} --rerun-triggers mtime $args
 
-    if [[ !skip_export_counts_drop ]]; then
+    if [[ $skip_export_counts_drop == false ]]; then
         snakemake exportCounts --cores 1
         mkdir -p exported_counts
         cp sample_annotation.tsv exported_counts/.
@@ -80,7 +80,7 @@ process DROP_CONFIG_RUN_AS {
     touch FRASER_results_fraser--.tsv
     touch gene_name_mapping_.tsv
     mkdir output
-    if [[ !skip_export_counts_drop ]]; then
+    if [[ $skip_export_counts_drop == false ]]; then
         mkdir exported_counts
     fi