From cc9368ee527243fc1809f891154ae0eb569887f3 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 24 Mar 2022 15:35:09 +0100
Subject: [PATCH] Prettier linting and update schema

---
 nextflow.config          |  2 +-
 nextflow_schema.json     | 48 ++++++++++++++++++++++++++++++++++++----
 workflows/taxprofiler.nf |  3 ++-
 3 files changed, 47 insertions(+), 6 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 5f7aec6..cc77a99 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -56,7 +56,7 @@ params {
 
     // FASTQ preprocessing
     shortread_clipmerge           = false
-    shortread_excludeunmerged        = true
+    shortread_excludeunmerged     = true
     longread_clip                 = false
 
     // MALT
diff --git a/nextflow_schema.json b/nextflow_schema.json
index de1e515..03910e9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "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",
@@ -173,7 +176,14 @@
                     "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": {
@@ -256,5 +266,35 @@
         {
             "$ref": "#/definitions/generic_options"
         }
-    ]
-}
+    ],
+    "properties": {
+        "databases": {
+            "type": "string",
+            "default": null
+        },
+        "shortread_clipmerge": {
+            "type": "string",
+            "default": "false"
+        },
+        "shortread_excludeunmerged": {
+            "type": "string",
+            "default": "true"
+        },
+        "longread_clip": {
+            "type": "string",
+            "default": "false"
+        },
+        "run_malt": {
+            "type": "string",
+            "default": "false"
+        },
+        "malt_mode": {
+            "type": "string",
+            "default": "BlastN"
+        },
+        "run_kraken2": {
+            "type": "string",
+            "default": "false"
+        }
+    }
+}
\ No newline at end of file
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 7320922..29058e6 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -88,8 +88,9 @@ workflow TAXPROFILER {
     //
     // MODULE: Run FastQC
     //
+    ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
     FASTQC (
-        INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
+        ch_input_for_fastqc
     )
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())