Revert "refactor: Move ld_library_path to env since we're using it an…

…yways now"

This reverts commit 074a97a.

modules/nf-core/sentieon/bwamem/main.nf

@@ -22,6 +22,15 @@ process SENTIEON_BWAMEM {
     task.ext.when == null || task.ext.when
 
     script:
+    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
+    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
+    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
+    if (workflow.containerEngine in ['singularity','apptainer']) {
+        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
+    } else {
+        fix_ld_library_path = ''
+    }
+
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
@@ -35,6 +44,8 @@ process SENTIEON_BWAMEM {
         echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
     fi
 
+    $fix_ld_library_path
+
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
 
     sentieon bwa mem \\
@@ -52,8 +63,19 @@ process SENTIEON_BWAMEM {
     """
 
     stub:
+    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
+    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
+    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
+    if (workflow.containerEngine in ['singularity','apptainer']) {
+        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
+    } else {
+        fix_ld_library_path = ''
+    }
+
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    $fix_ld_library_path
+
     touch ${prefix}.bam
     touch ${prefix}.bam.bai
 

modules/nf-core/sentieon/bwamem/tests/nextflow.config

@@ -6,13 +6,6 @@ env {
     SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA
     // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file
     // SENTIEON_LICENSE_BASE64 = secrets.SENTIEON_LICENSE_BASE64
-
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        LD_LIBRARY_PATH ="/usr/local/lib/:\$LD_LIBRARY_PATH;"
-    }
 }
 
 process {