Move MetaPhlAn3 to a subcommand and add mergemetaphlantables (#2026)

* Move MetaPhlAn3 to a subcommand and add mergemetaphlantables

* Add mergemetaphlantables tests

* Add mergemetaphlantables to test config

* Apply suggestions from code review

* Revert now unnecessary input channel name change and now document

* Update modules/metaphlan3/mergemetaphlantables/main.nf

* Require database directory and more details in description

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/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"

modules/metaphlan3/metaphlan3/main.nf

@@ -28,15 +28,18 @@ process METAPHLAN3 {
     def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
 
     """
+    BT2_DB=`find -L "${metaphlan_db}" -name "*rev.1.bt2" -exec dirname {} \\;`
+
     metaphlan \\
         --nproc $task.cpus \\
         $input_type \\
         $input_data \\
         $args \\
         $bowtie2_out \\
-        --bowtie2db ${metaphlan_db} \\
+        --bowtie2db \$BT2_DB \\
         --biom ${prefix}.biom \\
         --output_file ${prefix}_profile.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')

modules/metaphlan3/metaphlan3/meta.yml

@@ -24,6 +24,12 @@ input:
       type: file
       description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
       pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
+  - metaphlan_db:
+      type: file
+      description: |
+        Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.
+        Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!
+      pattern: "*/"
 
 output:
   - meta:

tests/config/pytest_modules.yml

@@ -1534,9 +1534,13 @@ metabat2/metabat2:
   - modules/metabat2/metabat2/**
   - tests/modules/metabat2/metabat2/**
 
-metaphlan3:
-  - modules/metaphlan3/**
-  - tests/modules/metaphlan3/**
+metaphlan3/metaphlan3:
+  - modules/metaphlan3/metaphlan3/**
+  - tests/modules/metaphlan3/metaphlan3/**
+
+metaphlan3/mergemetaphlantables:
+  - modules/metaphlan3/mergemetaphlantables/**
+  - tests/modules/metaphlan3/mergemetaphlantables/**
 
 methyldackel/extract:
   - modules/methyldackel/extract/**

tests/modules/metaphlan3/mergemetaphlantables/main.nf

@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR                           } from '../../../../modules/untar/main.nf'
+include { METAPHLAN3                      } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
+include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../modules/metaphlan3/mergemetaphlantables/main.nf'
+
+workflow test_metaphlan3_mergemetaphlantables {
+
+    input = Channel.of(
+        [[ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]],
+        [[ id:'test2', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]]
+    )
+
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
+
+    UNTAR ( db )
+    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
+    METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN3.out.profile.map{it[1]}.collect() )
+
+}

tests/modules/metaphlan3/mergemetaphlantables/nextflow.config

@@ -2,10 +2,6 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: SAMTOOLS_VIEW {
-        ext.prefix = { "${meta.id}.sam" }
-    }
-
     withName: METAPHLAN3 {
         ext.args = '--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local'
     }

tests/modules/metaphlan3/mergemetaphlantables/test.yml

@@ -0,0 +1,8 @@
+- name: metaphlan3 mergemetaphlantables test_metaphlan3_mergemetaphlantables
+  command: nextflow run ./tests/modules/metaphlan3/mergemetaphlantables -entry test_metaphlan3_mergemetaphlantables -c ./tests/config/nextflow.config  -c ./tests/modules/metaphlan3/mergemetaphlantables/nextflow.config
+  tags:
+    - metaphlan3
+    - metaphlan3/mergemetaphlantables
+  files:
+    - path: output/metaphlan3/merged_abundance_table.txt
+      contains: ["clade_name	NCBI_tax_id	"]

tests/modules/metaphlan3/metaphlan3/main.nf

@@ -2,9 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { UNTAR          } from '../../../modules/untar/main.nf'
-include { SAMTOOLS_VIEW  } from '../../../modules/samtools/view/main.nf'
-include { METAPHLAN3     } from '../../../modules/metaphlan3/main.nf'
+include { UNTAR          } from '../../../../modules/untar/main.nf'
+include { METAPHLAN3     } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
 
 workflow test_metaphlan3_single_end {
 
@@ -18,6 +17,16 @@ workflow test_metaphlan3_single_end {
     METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
+workflow test_metaphlan3_single_end_nodb {
+
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+
+    UNTAR ( db )
+    METAPHLAN3 ( input, [] )
+}
+
 workflow test_metaphlan3_paired_end {
 
     input = [ [ id:'test', single_end:false ], // meta map

tests/modules/metaphlan3/metaphlan3/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: METAPHLAN3 {
+        ext.args = '--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local'
+    }
+
+}