From e18e68faa50031aedb931fd5f2034b2d6bb72a39 Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Fri, 24 Feb 2023 15:50:24 +0100
Subject: [PATCH] Apply review suggestion

---
 conf/modules.config  | 2 +-
 nextflow.config      | 2 +-
 nextflow_schema.json | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 2b65798..e49d792 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -546,7 +546,7 @@ process {
         ext.args =  {
             [
                 "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
-                params.taxpasta_taxonomy_files ? "--taxonomy" : "",
+                params.taxpasta_taxonomy_dir ? "--taxonomy" ${params.taxpasta_taxonomy_dir}" : "",
             ].join(' ').trim()
             }
         publishDir = [
diff --git a/nextflow.config b/nextflow.config
index 30f2498..79f1d71 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -157,7 +157,7 @@ params {
     // profile standardisation
     run_profile_standardisation             = false
     standardisation_taxpasta_format         = 'tsv'
-    taxpasta_taxonomy_files                 = false
+    taxpasta_taxonomy_dir                   = false
     standardisation_motus_generatebiom      = false
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 78260a5..303ab5c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -517,7 +517,7 @@
                     "description": "The desired output format.",
                     "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
                 },
-                "taxpasta_taxonomy_files": {
+                "taxpasta_taxonomy_dir": {
                     "type": "boolean",
                     "description": "The path to a directory containing taxdump files.",
                     "help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."