fix tests

Author: junjun-zhang

cleanup-workdir/tests/checker.nf

@@ -20,22 +20,7 @@
     Junjun Zhang
 */
 
-/*
- This is an auto-generated checker workflow to test the generated main template workflow, it's
- meant to illustrate how testing works. Please update to suit your own needs.
-*/
-
-/********************************************************************/
-/* this block is auto-generated based on info from pkg.json where   */
-/* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '1.0.0'  // package version
-
-container = [
-    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.cleanup-workdir'
-]
-default_container_registry = 'ghcr.io'
-/********************************************************************/
 
 // universal params
 params.container_registry = ""
@@ -98,7 +83,7 @@ workflow {
     // perform cleanup in gFile1 workdir
     cleanupWorkdir(
         gFile1.out.collect(),
-        gFile2.out.file.collect()  // flag enables waiting for gFile2 before cleaning up gFile1 workdir
+        fExist1.out.collect()  // flag enables waiting for fExist1 before cleaning up gFile1 workdir
     )
 
     // test cleaned up workdir from gFile1 indeed does not have previous files

cleanup-workdir/tests/files-exist.nf

@@ -29,7 +29,7 @@ nextflow.enable.dsl = 2
 version = '1.0.0'  // package version
 
 container = [
-    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.helper-functions'
+    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.cleanup-workdir'
 ]
 default_container_registry = 'ghcr.io'
 /********************************************************************/
@@ -49,23 +49,29 @@ process filesExist {
         path files
         val dependency_flag  // any output from process(es) you'd like to make this process depend on
 
+    output:
+        stdout()
+
     script:
         file_name_arg = file_names instanceof List ? file_names.join(" ") : file_names
         """
         if [[ "${expect}" = "exist"  ]]; then
             for f in \$(echo "${file_name_arg}"); do
                 if [[ ! -f \$f ]]; then
-                    exit "Expected \$f not exists."
+                    echo "Expected \$f not exists."
+                    exit 1
                 fi
             done
         elif [[ "${expect}" = "not_exist"  ]]; then
             for f in \$(echo "${file_name_arg}"); do
                 if [[ -f \$f ]]; then
-                    exit "Unexpected \$f exists."
+                    echo "Unexpected \$f exists."
+                    exit 1
                 fi
             done
         else
-            exit "Second argument must be either 'exist' or 'not_exist'. '${expect}' is supplied."
+            echo "Second argument must be either 'exist' or 'not_exist'. '${expect}' is supplied."
+            exit 1
         fi
         """
 }

cleanup-workdir/tests/generate-dummy-file.nf

@@ -29,7 +29,7 @@ nextflow.enable.dsl = 2
 version = '1.0.0'  // package version
 
 container = [
-    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.helper-functions'
+    'ghcr.io': 'ghcr.io/icgc-argo/data-processing-utility-tools.cleanup-workdir'
 ]
 default_container_registry = 'ghcr.io'
 /********************************************************************/