Updated nextflow_schema.json, modules.json, and modules.config files

phac-nml · Apr 10, 2024 · a5f1ebc · a5f1ebc
1 parent 9266173
commit a5f1ebc
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Showing 3 changed files with 7 additions and 29 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -12,10 +12,6 @@
 
 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,
@@ -30,30 +26,6 @@ process {
         ]
     }
 
-    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/modules.json b/modules.json
@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "csvtk/concat": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -57,7 +57,8 @@
                     "format": "directory-path",
                     "description": "Path to Bracken database (do not use symlinks)"
                 }
-            }
+            },
+            "required": ["kraken2_db", "bracken_db"]
         },
         "speciesabundance_pipeline_parameters": {
             "title": "SpeciesAbundance Pipeline Parameters",