From f0aa89cb877513034e7202f6a977f5f79a86f0df Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Fri, 17 Feb 2023 14:47:29 +0100
Subject: [PATCH] Rename taxpasta parameters and remove samplesheet parameter

---
 conf/modules.config  |  7 +++----
 nextflow.config      |  7 +++----
 nextflow_schema.json | 25 ++++++++++---------------
 3 files changed, 16 insertions(+), 23 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 4a1fba2..0bab02b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -534,7 +534,7 @@ process {
     }
 
     withName: MOTUS_MERGE {
-        ext.args = { params.generate_biom_output ? "-B" : "" }
+        ext.args = { params.standardisation_motus_generatebiom ? "-B" : "" }
         ext.prefix = { "motus_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/motus/" },
@@ -545,9 +545,8 @@ process {
     withName: TAXPASTA_MERGE {
         ext.args =  {
             [
-                "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}",
-                params.taxpasta_add_taxonomy ? "-p" : "",
-                params.taxpasta_add_samplesheet ? "-s" :""
+                "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
+                params.standardisation_taxpasta_addtaxonomy ? "-p" : ""
             ].join(' ').trim()
             }
         publishDir = [
diff --git a/nextflow.config b/nextflow.config
index 9d3af4c..34e8b00 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -156,10 +156,9 @@ params {
 
     // profile standardisation
     run_profile_standardisation             = false
-    taxpasta_add_taxonomy                   = false
-    taxpasta_add_samplesheet                = false
-    taxpasta_standardisation_format         = 'tsv'
-    generate_biom_output                    = false
+    standardisation_taxpasta_addtaxonomy    = false
+    standardisation_taxpasta_format         = 'tsv'
+    standardisation_motus_generatebiom      = false
 }
 
 // Load base.config by default for all pipelines
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 80ba987..a7a1b4d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -491,11 +491,11 @@
                     "description": "Turn on standardisation of taxon tables across profilers",
                     "help_text": "Turns on standardisation of output OTU tables across all tools; each into a TSV format following the following scheme:\n\n|TAXON   | SAMPLE_A | SAMPLE_B |\n|-------------|----------------|-----------------|\n| taxon_a | 32               | 123             |\n| taxon_b | 1                 | 5                 |\n\nThis currently only is generated for mOTUs."
                 },
-                "generate_biom_output": {
+                "standardisation_motus_generatebiom": {
                     "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on generation of BIOM output (currently only applies to mOTUs)",
-                    "help_text": "Turn on the saving of the taxonomic output in BIOM format (`.biom`) in the results directory of your pipeline run, instead of the default TSV format.\n\nNote this file is from the output of the `motus merge` command.\n\n> Modifies tool parameter(s):\n> - `-B -o`"
+                    "help_text": "Turn on the saving of the taxonomic output in BIOM format (`.biom`) in the results directory of your pipeline run, instead of the default TSV format.\\n\\nNote this file is from the output of the `motus merge` command.\\n\\n> Modifies tool parameter(s):\\n> - `-B -o`"
                 },
                 "run_krona": {
                     "type": "boolean",
@@ -510,22 +510,17 @@
                     "description": "Specify path to krona taxonomy directories (required for MALT krona plots)",
                     "help_text": "Specify a path to a Krona taxonomy database directory (i.e. a directory containing a krona generated `.tab` file).\n\nThis is only required for generating Krona plots of MALT output.\n\nNote this taxonomy database must be downloaded and generated with the `updateTaxonomy.sh` script from the krona-tools package."
                 },
-                "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."
-                },
-                "taxpasta_add_samplesheet": {
-                    "type": "boolean",
-                    "description": "A table with with two columns, one for the sample and one for  the taxonomic profile.",
-                    "help_text": "If this option is provided, any arguments are ignored."
-                },
-                "taxpasta_standardisation_format": {
+                "standardisation_taxpasta_format": {
                     "type": "string",
                     "default": "tsv",
+                    "fa_icon": "fas fa-file",
                     "description": "The desired output format.",
-                    "enum": ["tsv", "csv", "arrow", "parquet", "biom"],
-                    "fa_icon": "fas fa-file"
+                    "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
+                },
+                "standardisation_taxpasta_addtaxonomy": {
+                    "type": "boolean",
+                    "description": "The path to a directory containing taxdump files, typically from NCBI.",
+                    "help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."
                 }
             },
             "fa_icon": "fas fa-chart-line"