Start works - need updated module though t have meta

conf/modules.config

@@ -327,7 +327,7 @@ process {
         ]
     }
 
-    withName: METAPHLAN3 {
+    withName: METAPHLAN3_METAPHLAN3 {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
@@ -337,6 +337,15 @@ process {
         ]
     }
 
+    withName: METAPHLAN3_MERGEMETAPHLANTABLES {
+        ext.prefix = { "${meta.id}_combined_reports" }
+        publishDir = [
+            path: { "${params.outdir}/metaphlan3/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{txt}'
+        ]
+    }
+
     withName: CENTRIFUGE_CENTRIFUGE {
         publishDir = [
             path: { "${params.outdir}/centrifuge/${meta.db_name}/" },

modules.json

@@ -94,6 +94,10 @@
                     "branch": "master",
                     "git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
                 },
+                "metaphlan3/mergemetaphlantables": {
+                    "branch": "master",
+                    "git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"
+                },
                 "metaphlan3/metaphlan3": {
                     "branch": "master",
                     "git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"

modules/nf-core/modules/metaphlan3/mergemetaphlantables/main.nf

@@ -0,0 +1,33 @@
+process METAPHLAN3_MERGEMETAPHLANTABLES {
+    label 'process_single'
+
+    conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
+        'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
+
+    input:
+    path(profiles)
+
+    output:
+    tuple path("${prefix}.txt") , emit: txt
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "merged_abundance_table"
+    """
+    merge_metaphlan_tables.py \\
+        $args \\
+        -o ${prefix}.txt \\
+        ${profiles}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
+    END_VERSIONS
+    """
+}

modules/nf-core/modules/metaphlan3/mergemetaphlantables/meta.yml

@@ -0,0 +1,34 @@
+name: "metaphlan3_mergemetaphlantables"
+description: Merges output abundance tables from MetaPhlAn3
+keywords:
+  - metagenomics
+  - classification
+  - merge
+  - table
+  - profiles
+tools:
+  - metaphlan3:
+      description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
+      homepage: https://huttenhower.sph.harvard.edu/metaphlan/
+      documentation: https://github.com/biobakery/MetaPhlAn
+      doi: "10.7554/eLife.65088"
+      licence: ["MIT License"]
+
+input:
+  - profiles:
+      type: file
+      description: List of per-sample MetaPhlAn3 taxonomic abundance tables
+      pattern: "*"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - txt:
+      type: txt
+      description: Combined MetaPhlAn3 table
+      pattern: "*.txt"
+
+authors:
+  - "@jfy133"

subworkflows/local/standardisation_profiles.nf

@@ -2,8 +2,9 @@
 // Standardise output files e.g. aggregation
 //
 
-include { KAIJU_KAIJU2TABLE                     } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
-include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
+include { KAIJU_KAIJU2TABLE               } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
+include { MOTUS_MERGE                     } from '../../modules/nf-core/modules/motus/merge/main'
+include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/modules/metaphlan3/mergemetaphlantables/main'
 
 workflow STANDARDISATION_PROFILES {
     take:
@@ -23,6 +24,7 @@ workflow STANDARDISATION_PROFILES {
     ch_input_profiles = profiles
         .branch {
             motus: it[0]['tool'] == 'motus'
+            metaphlan3: it[0]['tool'] == 'metaphlan3'
             unknown: true
         }
 
@@ -58,6 +60,21 @@ workflow STANDARDISATION_PROFILES {
     ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
     ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
 
+    // MetaPhlAn3
+    ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3
+                            .map { [it[0]['db_name'], it[1]] }
+                            .groupTuple()
+                            .map {
+                                [it[1]]
+                            }
+
+    METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 )
+    ch_standardised_tables = ch_standardised_tables.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
+    ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
+    ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
+
+    // mOTUs
+
     // mOTUs has a 'single' database, and cannot create custom ones.
     // Therefore removing db info here, and publish merged at root mOTUs results
     // directory