Removed unneeded config in modules

phac-nml · Jan 25, 2024 · 13a4284 · 13a4284
1 parent ba17901
commit 13a4284
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Showing 2 changed files with 1 addition and 37 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -12,48 +12,12 @@
 
 process {
 
-    // Publish directory names
-    assembly_directory_name = "assembly"
-    summary_directory_name = "summary"
-
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: ASSEMBLY_STUB {
-        publishDir = [
-            path: { ["${params.outdir}", "${task.assembly_directory_name}"].join(File.separator) },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: GENERATE_SUMMARY {
-        publishDir = [
-            path: { ["${params.outdir}", "${task.summary_directory_name}"].join(File.separator) },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: IRIDA_NEXT_OUTPUT {
-        publishDir = [
-            path: { "${params.outdir}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv'
+    input = 'https://raw.githubusercontent.com/phac-nml/fetchdatairidanext/dev/assets/samplesheet.csv'
 }