From 982fba1b5849f458806ad0ef10afc5fdc33807ef Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 11 May 2023 14:13:18 +0200
Subject: [PATCH] Fix taxpasta not receiving taxonomy directory

---
 CHANGELOG.md                                   | 12 ++++++++++++
 conf/modules.config                            |  1 -
 subworkflows/local/standardisation_profiles.nf |  2 +-
 3 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c055527..9858ab9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1 - Dodgy Dachshund Patch [2023-05-11]
+
+### `Added`
+
+### `Fixed`
+
+- [#291](https://github.com/nf-core/taxprofiler/pull/291) - Fix Taxpasta not receiving taxonomy directory (❤️ to SannaAb for reporting, fix by @jfy133)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.0.0 - Dodgy Dachshund [2023-03-13]
 
 Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.
diff --git a/conf/modules.config b/conf/modules.config
index ee1a3d2..301ec9a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -543,7 +543,6 @@ process {
         ext.args =  {
             [
                 "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
-                params.taxpasta_taxonomy_dir ? "--taxonomy ${params.taxpasta_taxonomy_dir}" : "",
                 params.taxpasta_add_name ?  "--add-name" : "",
                 params.taxpasta_add_rank ? "--add-rank" : "",
                 params.taxpasta_add_lineage ? "--add-lineage" : "",
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
index 26355b7..dde76c8 100644
--- a/subworkflows/local/standardisation_profiles.nf
+++ b/subworkflows/local/standardisation_profiles.nf
@@ -33,7 +33,7 @@ workflow STANDARDISATION_PROFILES {
                             .groupTuple ()
                             .map { [ it[0], it[1].flatten() ] }
 
-    TAXPASTA_MERGE (ch_input_for_taxpasta, [], [])
+    TAXPASTA_MERGE (ch_input_for_taxpasta, params.taxpasta_taxonomy_dir ? params.taxpasta_taxonomy_dir : [], [])
 
     /*
         Split profile results based on tool they come from