Formatting and fix fastp output

nextflow_schema.json

@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -176,14 +173,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -298,10 +288,7 @@
         "shortread_clipmerge_tool": {
             "type": "string",
             "default": "fastp",
-            "enum": [
-                "fastp",
-                "adapterremoval"
-            ]
+            "enum": ["fastp", "adapterremoval"]
         },
         "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"
@@ -345,10 +332,7 @@
         "shortread_complexityfilter_prinseqplusplus_mode": {
             "type": "string",
             "default": "entropy",
-            "enum": [
-                "entropy",
-                "dust"
-            ]
+            "enum": ["entropy", "dust"]
         },
         "shortread_complexityfilter_prinseqplusplus_dustscore": {
             "type": "number",
@@ -364,4 +348,4 @@
             "type": "boolean"
         }
     }
-}
+}

subworkflows/local/shortread_adapterremoval.nf

@@ -67,7 +67,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                 [meta_new, reads]
             }
             .groupTuple()
-            .map { meta, fastq -> [meta, fastq.flatten()] }
+            .map { meta, fastq -> [meta, [ fastq ].flatten()] }
 
 
         CAT_FASTQ(ch_concat_fastq)