Move config for containers out into the config files instead of main.nf

workflow/configs/biohpc_docker.config

@@ -6,4 +6,13 @@ docker {
 
 process {
     executor = 'local'
+    withName:uppercase {
+        container = 'ubuntu:latest'
+    }
+    withName:tolines {
+        container = 'ubuntu:latest'
+    }
+    withName:wordcounts {
+        container = 'ubuntu:latest'
+    }
 }

workflow/configs/biohpc_singularity.config

@@ -6,4 +6,13 @@ singularity {
 
 process {
     executor = 'local'
+    withName:uppercase {
+        container = 'ubuntu:latest'
+    }
+    withName:tolines {
+        container = 'ubuntu:latest'
+    }
+    withName:wordcounts {
+        container = 'ubuntu:latest'
+    }
 }

workflow/main.nf

@@ -46,7 +46,6 @@ process parameters {
 process uppercase {
 
     cpus 1
-    container 'ubuntu:latest'
 
     input:
     file story from stories
@@ -63,7 +62,6 @@ process uppercase {
 process tolines {
 
     cpus 1
-    container 'ubuntu:latest'
 
     input:
     file uppercase from uppercased
@@ -79,7 +77,6 @@ process tolines {
 
 process wordcounts {
 
-    container 'ubuntu:latest'
 
     // Publish the outputs we create here into the workflow output directory
     publishDir "$baseDir/output", mode: 'copy'