new module: kaiju/mkfmi (nf-core#4125)

* new module: kaiju/mkfmi * local tests * Update modules/nf-core/kaiju/mkfmi/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/kaiju/mkfmi/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> * Update modules/nf-core/kaiju/mkfmi/meta.yml Co-authored-by: James A. Fellows Yates <[email protected]> --------- Co-authored-by: James A. Fellows Yates <[email protected]>
adamrtalbot · Oct 26, 2023 · 7365564 · 7365564
1 parent bb0fc44
commit 7365564
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diff --git a/modules/nf-core/kaiju/mkfmi/main.nf b/modules/nf-core/kaiju/mkfmi/main.nf
@@ -0,0 +1,36 @@
+process KAIJU_MKFMI {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "bioconda::kaiju=1.9.2"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/kaiju:1.9.2--h5b5514e_0':
+        'biocontainers/kaiju:1.9.2--h5b5514e_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.fmi"), emit: fmi
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    kaiju-mkbwt \\
+        $args \\
+        -n $task.cpus \\
+        -o ${prefix} \\
+        ${fasta}
+    kaiju-mkfmi ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/kaiju/mkfmi/meta.yml b/modules/nf-core/kaiju/mkfmi/meta.yml
@@ -0,0 +1,44 @@
+name: "kaiju_mkfmi"
+description: Make Kaiju FMI-index file from a protein FASTA file
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+  - database
+  - index
+tools:
+  - "kaiju":
+      description: "Fast and sensitive taxonomic classification for metagenomics"
+      homepage: "https://bioinformatics-centre.github.io/kaiju/"
+      documentation: "https://github.com/bioinformatics-centre/kaiju/blob/master/README.md"
+      tool_dev_url: "https://github.com/bioinformatics-centre/kaiju"
+      doi: "10.1038/ncomms11257"
+      licence: ["GNU GPL v3"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - fasta:
+      type: file
+      description: Uncompressed Protein FASTA file (mandatory)
+      pattern: "*.{fa,faa,fasta}"
+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
+      pattern: "versions.yml"
+  - fmi:
+      type: file
+      description: Kaiju FM-index file
+      pattern: "*.{fmi}"
+
+authors:
+  - "@alxndrdiaz"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1936,6 +1936,10 @@ kaiju/kaiju2table:
   - modules/nf-core/kaiju/kaiju2table/**
   - tests/modules/nf-core/kaiju/kaiju2table/**
 
+kaiju/mkfmi:
+  - modules/nf-core/kaiju/mkfmi/**
+  - tests/modules/nf-core/kaiju/mkfmi/**
+
 kalign/align:
   - modules/nf-core/kalign/align/**
   - tests/modules/nf-core/kalign/align/**

diff --git a/tests/modules/nf-core/kaiju/mkfmi/main.nf b/tests/modules/nf-core/kaiju/mkfmi/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KAIJU_MKFMI } from '../../../../../modules/nf-core/kaiju/mkfmi/main.nf'
+
+workflow test_kaiju_mkfmi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+    ]
+
+    KAIJU_MKFMI ( input )
+}
diff --git a/tests/modules/nf-core/kaiju/mkfmi/nextflow.config b/tests/modules/nf-core/kaiju/mkfmi/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: KAIJU_MKFMI {
+        ext.args = '-a ACDEFGHIKLMNPQRSTVWY'
+    }
+
+}
diff --git a/tests/modules/nf-core/kaiju/mkfmi/test.yml b/tests/modules/nf-core/kaiju/mkfmi/test.yml
@@ -0,0 +1,9 @@
+- name: kaiju mkfmi test_kaiju_mkfmi
+  command: nextflow run ./tests/modules/nf-core/kaiju/mkfmi -entry test_kaiju_mkfmi -c ./tests/config/nextflow.config
+  tags:
+    - kaiju/mkfmi
+    - kaiju
+  files:
+    - path: output/kaiju/test.fmi
+      md5sum: 05615794180a9c2e739a9bf1c24c99d5
+    - path: output/kaiju/versions.yml