Merge pull request #31 from U-BDS/dev

Closing issue #30 by exporting home in process
nf-core · Aug 30, 2024 · af8cf74 · af8cf74
2 parents ddb0c28 + 9baef2a
commit af8cf74
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/modules/local/isoquant.nf b/modules/local/isoquant.nf
@@ -26,8 +26,11 @@ process ISOQUANT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
+    // setting custom home via export (see issue #30)
     if ( !group_category?.trim() ){
         """
+        export HOME=\$(pwd)
+
         isoquant.py ${args} \\
                     --threads $task.cpus \\
                     --datatype nanopore \\
@@ -46,6 +49,8 @@ process ISOQUANT {
         """
     } else {
         """
+        export HOME=\$(pwd)
+
         isoquant.py ${args} \\
                     --threads $task.cpus \\
                     --data_type nanopore \\

diff --git a/nextflow.config b/nextflow.config
@@ -146,10 +146,10 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
-        docker.runOptions       = '-u $(id -u):$(id -g) -e HOME=$(pwd)'
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64 -e HOME=$(pwd)'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled     = true