From b87f780c9f2dee6bd11bacb0402031ca6a6c830c Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 9 Oct 2024 10:40:46 +0200
Subject: [PATCH] Apply suggestions from code review

---
 assets/schema_input.json | 3 +++
 docs/output.md           | 1 -
 nextflow.config          | 3 +--
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index d72dd4e..3ff51c0 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -10,11 +10,13 @@
             "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
+                "uniqueItems": true,
                 "errorMessage": "Sequence reference name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
             "taxid": {
                 "type": "integer",
+                "uniqueItems": true,
                 "errorMessage": "Please provide a valid taxonomic ID in integer format",
                 "meta": ["taxid"]
             },
@@ -30,6 +32,7 @@
                         "maxLength": 0
                     }
                 ],
+                "uniqueItems": true,
                 "errorMessage": "FASTA file for nucleotide sequence cannot contain spaces and must have a valid FASTA extension (fasta, fna, fa, fas, faa), optionally gzipped",
                 "exists": true,
                 "format": "file-path"
diff --git a/docs/output.md b/docs/output.md
index 691bb5c..9f5ddb0 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -13,7 +13,6 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
-
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 - [Bracken](#bracken) - Database files for Brakcen
 - [Centrifuge](#centrifuge) - Database files for Centrifuge
diff --git a/nextflow.config b/nextflow.config
index 3c4f616..1ca6c7f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -179,8 +179,7 @@ profiles {
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load nf-core/createtaxdb custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/createtaxdb.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/createtaxdb.config" : "/dev/null"
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers