From a4a9b161d80914f7f1964b4a86c58229d4d884b3 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 29 Apr 2022 22:02:44 +0200
Subject: [PATCH] Lintin

---
 conf/modules.config  |  4 ++--
 docs/usage.md        |  2 +-
 modules.json         |  2 +-
 nextflow_schema.json | 45 +++++++-------------------------------------
 4 files changed, 11 insertions(+), 42 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 9b081b5..d8fb382 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -274,7 +274,7 @@ process {
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
     }
 
-   withName: KAIJU_KAIJU2TABLE {
+    withName: KAIJU_KAIJU2TABLE {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
@@ -284,7 +284,7 @@ process {
         ]
     }
 
-   withName: DIAMOND_BLASTX {
+    withName: DIAMOND_BLASTX {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
diff --git a/docs/usage.md b/docs/usage.md
index 002f4f2..cee2bb6 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -129,7 +129,7 @@ Expected (uncompressed) database files for each tool are as follows:
   - `nodes.dmp`
   - `names.dmp`
 - **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
-  to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options).  A file named:
+  to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
   - `<database_name>.dmnd`
 
 ## Running the pipeline
diff --git a/modules.json b/modules.json
index 7b659c1..a65926c 100644
--- a/modules.json
+++ b/modules.json
@@ -68,4 +68,4 @@
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index fc516d6..f429d1b 100644
--- a/nextflow_schema.json
+++ b/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": {
@@ -304,10 +294,7 @@
         "shortread_clipmerge_tool": {
             "type": "string",
             "default": "fastp",
-            "enum": [
-                "fastp",
-                "adapterremoval"
-            ]
+            "enum": ["fastp", "adapterremoval"]
         },
         "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"
@@ -348,10 +335,7 @@
         "shortread_complexityfilter_prinseqplusplus_mode": {
             "type": "string",
             "default": "entropy",
-            "enum": [
-                "entropy",
-                "dust"
-            ]
+            "enum": ["entropy", "dust"]
         },
         "shortread_complexityfilter_prinseqplusplus_dustscore": {
             "type": "number",
@@ -404,14 +388,7 @@
         "kaiju_taxon_name": {
             "type": "string",
             "default": "species",
-            "enum": [
-                "phylum",
-                "class",
-                "order",
-                "family",
-                "genus",
-                "species"
-            ]
+            "enum": ["phylum", "class", "order", "family", "genus", "species"]
         },
         "run_diamond": {
             "type": "boolean"
@@ -419,15 +396,7 @@
         "diamond_output_format": {
             "type": "string",
             "default": "tsv",
-            "enum": [
-                "blast",
-                "xml",
-                "txt",
-                "daa",
-                "sam",
-                "tsv",
-                "paf"
-            ]
+            "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
         }
     }
-}
\ No newline at end of file
+}