Added MetaPlAn subworkflow

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/main.nf

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+include { METAPHLAN_MAKEDB      } from '../../../modules/nf-core/metaphlan/makedb/main'
+include { METAPHLAN_METAPHLAN     } from '../../../modules/nf-core/metaphlan/metaphlan/main'
+include { METAPHLAN3_MERGEMETAPHLANTABLES     } from '../../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
+
+
+workflow FASTQ_TAXONOMIC_PROFILE_METAPHLAN {
+
+    take:
+    ch_fastq
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    METAPHLAN_MAKEDB ( )
+    ch_versions = ch_versions.mix(METAPHLAN_MAKEDB.out.versions.first())
+
+    METAPHLAN_METAPHLAN ( ch_fastq, METAPHLAN_MAKEDB.out.db )
+    ch_versions = ch_versions.mix(METAPHLAN_METAPHLAN.out.versions.first())
+
+    METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN_METAPHLAN.out.profile.map{ [ [id:'all_samples'], it[1] ] }.groupTuple( sort: 'deep') )
+    ch_versions = ch_versions.mix(METAPHLAN3_MERGEMETAPHLANTABLES.out.versions.first())
+
+    emit:
+    merged_taxa      = METAPHLAN3_MERGEMETAPHLANTABLES.out.txt
+
+
+    versions = ch_versions
+}
+

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/meta.yml

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+name: "fastq_taxonomic_profile_metaphlan"
+description: Subworkflow to taxonomically classify metagenomic sequencing data using MetaPhlAn
+keywords:
+  - metaphlan
+  - metagenomics
+  - database
+  - classification
+  - merge
+  - profiles
+components:
+  - metaphlan/makedb
+  - metaphlan/metaphlan
+  - metaphlan/mergemetaphlantables
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:‘test’, single_end:false ]
+  - ch_fastq:
+      type: file
+      description: |
+        The input channel containing the FASTQ files
+        Structure: [ val(meta), path(fastqs) ]
+      pattern: "*.{fastq/fastq.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:‘test’, single_end:false ]
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+  - txt:
+      type: file
+      description: |
+        Combined MetaPhlAn table
+        Structure: [ val(meta), path(txt) ]
+      pattern: "*.txt"
+
+authors:
+  - "@LaurenGonsalves"
+  - "@hhayden01"
+  - "@ErikLHendrickson"
+  - "@CarsonJM"
+maintainers:
+  - "@LaurenGonsalves"
+  - "@CarsonJM"

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/tests/main.nf.test

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+// nf-core subworkflows test fastq_taxonomic_profile_metaphlan
+nextflow_workflow {
+
+    name "Test Subworkflow FASTQ_TAXONOMIC_PROFILE_METAPHLAN"
+    script "../main.nf"
+    workflow "FASTQ_TAXONOMIC_PROFILE_METAPHLAN"
+    config "./nextflow.config"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/fastq_taxonomic_profile_metaphlan"
+    tag "metaphlan/makedb"
+    tag "metaphlan/metaphlan"
+    tag "metaphlan3/mergemetaphlantables"
+
+
+    test("sarscov2 - fastq - paired_end") {
+
+        when {
+            workflow {
+                """
+                // TODO nf-core: define inputs of the workflow here.
+                input[0] = Channel.of (
+                    [
+                        [ id:'test1', single_end:false ], // meta map
+                            [
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                            ]
+                    ],
+                    [
+                        [ id:'test2', single_end:false ], // meta map
+                            [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)
+                            ]
+                    ]
+                )
+
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out).match()}
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+    }
+}

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/tests/nextflow.config

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+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: METAPHLAN_MAKEDB {
+        ext.args = '--index mpa_vJan21_TOY_CHOCOPhlAnSGB_202103'
+    }
+
+}

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/tests/tags.yml

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+subworkflows/fastq_taxonomic_profile_metaphlan:
+  - subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/**