From 5a6fcf1f42a1c13cde747cf158afe4f2ed96486b Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Fri, 24 Feb 2023 11:44:07 +0100
Subject: [PATCH] Update taxpasta/merge to version 0.2.0 and add taxonomy
 argument

---
 conf/modules.config                    | 7 ++++++-
 modules.json                           | 2 +-
 modules/nf-core/taxpasta/merge/main.nf | 6 +++---
 nextflow.config                        | 1 +
 nextflow_schema.json                   | 5 +++++
 5 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 605a7c5..10ce34d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -543,7 +543,12 @@ process {
     }
 
     withName: TAXPASTA_MERGE {
-        ext.args =  { "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}" }
+        ext.args =  {
+            [
+                "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
+                params.taxpasta_add_taxonomy ? "--taxonomy" : "",
+            ].join(' ').trim()
+            }
         publishDir = [
             path: { "${params.outdir}/taxpasta/" },
             mode: params.publish_dir_mode,
diff --git a/modules.json b/modules.json
index 5b07b07..d1899a4 100644
--- a/modules.json
+++ b/modules.json
@@ -209,7 +209,7 @@
                     },
                     "taxpasta/merge": {
                         "branch": "master",
-                        "git_sha": "74ab450ed05e034d049c00f6e2853de2c31594b4",
+                        "git_sha": "fe58454add6225d2b7468e6d72a3a1f6a3149638",
                         "installed_by": ["modules"]
                     },
                     "untar": {
diff --git a/modules/nf-core/taxpasta/merge/main.nf b/modules/nf-core/taxpasta/merge/main.nf
index 67a6f25..46aea29 100644
--- a/modules/nf-core/taxpasta/merge/main.nf
+++ b/modules/nf-core/taxpasta/merge/main.nf
@@ -2,10 +2,10 @@ process TAXPASTA_MERGE {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::taxpasta=0.1.1"
+    conda "bioconda::taxpasta=0.2.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/taxpasta:0.1.1--pyhdfd78af_0':
-        'quay.io/biocontainers/taxpasta:0.1.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/taxpasta:0.2.0--pyhdfd78af_0':
+        'quay.io/biocontainers/taxpasta:0.2.0--pyhdfd78af_0' }"
 
 
     input:
diff --git a/nextflow.config b/nextflow.config
index 9228d67..18e706a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -157,6 +157,7 @@ params {
     // profile standardisation
     run_profile_standardisation             = false
     standardisation_taxpasta_format         = 'tsv'
+    taxpasta_add_taxonomy                   = false
     standardisation_motus_generatebiom      = false
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3de42d5..314b485 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -516,6 +516,11 @@
                     "fa_icon": "fas fa-file",
                     "description": "The desired output format.",
                     "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
+                },
+                "taxpasta_add_taxonomy": {
+                    "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."
                 }
             },
             "fa_icon": "fas fa-chart-line"