fix: Escape '$' for cmd interpolation

mskilab-org · Oct 18, 2023 · 5c20423 · 5c20423
1 parent e18903d
commit 5c20423
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 9 deletions.
diff --git a/modules/local/dryclean/main.nf b/modules/local/dryclean/main.nf
@@ -34,6 +34,7 @@ process DRYCLEAN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    #!/bin/bash
     set -o allexport
     # Check if the environment has the module program installed
     if command -v module &> /dev/null
@@ -59,12 +60,12 @@ process DRYCLEAN {
     set +x
 
     ## find R installation and dryclean exec
-    echo "USING LIBRARIES: $(Rscript -e 'print(.libPaths())')"
-    export drycleanPath=$(Rscript -e 'cat(suppressWarnings(find.package("dryclean")))')
+    echo "USING LIBRARIES: \$(Rscript -e 'print(.libPaths())')"
+    export drycleanPath=\$(Rscript -e 'cat(suppressWarnings(find.package("dryclean")))')
     export drycln=$drycleanPath/extdata/drcln
     echo $drycln
     set +x
-    CMD="Rscript $drycln $@"
+    CMD="Rscript $drycln \$@"
 
     if [ ! -s ./drycleaned.cov.rds ]; then
 	if ! { echo "Running:" && echo "${CMD}" && eval ${CMD}; }; then

diff --git a/modules/local/jabba/main.nf b/modules/local/jabba/main.nf
@@ -60,6 +60,8 @@ process JABBA {
     //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
     //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
     """
+    #!/bin/bash
+
     set -o allexport
 
     # Check if the environment has the module program installed
@@ -86,17 +88,17 @@ process JABBA {
     R_PROFILE_USER="/dev/null"
 
     ## find R installation
-    echo "USING LIBRARIES: $(Rscript -e 'print(.libPaths())')"
+    echo "USING LIBRARIES: \$(Rscript -e 'print(.libPaths())')"
 
-    export jabPath=$(Rscript -e 'cat(suppressWarnings(find.package("JaBbA")))')
+    export jabPath=\$(Rscript -e 'cat(suppressWarnings(find.package("JaBbA")))')
     export jba=$jabPath/extdata/jba
     echo $jba
     set +x
 
-    export cmd="Rscript $jba $@"
+    export cmd="Rscript $jba \$@"
 
-    { echo "Running:" && echo "$(echo $cmd)" && echo && eval $cmd; }
-    cmdsig=$?
+    { echo "Running:" && echo "\$(echo $cmd)" && echo && eval $cmd; }
+    cmdsig=\$?
     if [ "$cmdsig" = 0 ]; then
         echo "Finish!"
     else
@@ -110,7 +112,7 @@ process JABBA {
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    
+
     """
     touch jabba.simple.rds
     touch jabba.simple.gg.rds