Apply review suggestions

conf/modules.config

@@ -548,7 +548,7 @@ process {
                 "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}",
                 params.taxpasta_add_taxonomy ? "-p" : "",
                 params.taxpasta_add_samplesheet ? "-s" :""
-            ].join(',').replaceAll(','," ")
+            ].join(' ').trim()
             }
         publishDir = [
             path: { "${params.outdir}/taxpasta/" },

conf/test.config

@@ -33,7 +33,7 @@ params {
     run_kaiju                             = true
     run_kraken2                           = true
     run_bracken                           = true
-    run_malt                              = false
+    run_malt                              = true
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true

docs/output.md

@@ -33,7 +33,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [MALT](#malt) - Sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics
 - [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier
 - [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
-- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples for the same classifier/profiler.
+- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples from the same database and classifier/profiler.
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -438,7 +438,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
 
 ### TAXPASTA
 
-[TAXPASTA](https://github.com/taxprofiler/taxpasta) is a python package added as a module in nf-core/taxprofiler that can standardise and merge two or more taxonomic profiles across samples into one single table..
+[TAXPASTA](https://github.com/taxprofiler/taxpasta) that standardises and merge two or more taxonomic profiles across samples into one single table. It supports multiple different classifiers simplifying taxonomic classification results between tools and databases.
 
 <details markdown="1">
 <summary>Output files</summary>

nextflow_schema.json

@@ -523,7 +523,8 @@
                 "taxpasta_standardisation_format": {
                     "type": "string",
                     "default": "tsv",
-                    "description": "The desired output format."
+                    "description": "The desired output format.",
+                    "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
                 }
             },
             "fa_icon": "fas fa-chart-line"

subworkflows/local/standardisation_profiles.nf

@@ -90,7 +90,6 @@ workflow STANDARDISATION_PROFILES {
                                 }
 
 
-
     KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
     ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
     ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
@@ -142,7 +141,6 @@ workflow STANDARDISATION_PROFILES {
     ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
     ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
 
-    ch_standardised_tables.dump (tag: 'standardised')
 
     // mOTUs