add module for legsta (#1319)

modules/legsta/main.nf

@@ -0,0 +1,33 @@
+process LEGSTA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2':
+        'quay.io/biocontainers/legsta:0.5.1--hdfd78af_2' }"
+
+    input:
+    tuple val(meta), path(seqs)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    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}"
+    """
+    legsta \\
+        $args \\
+        $seqs > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;')
+    END_VERSIONS
+    """
+}

modules/legsta/meta.yml

@@ -0,0 +1,42 @@
+name: legsta
+description: Typing of clinical and environmental isolates of Legionella pneumophila
+keywords:
+  - bacteria
+  - legionella
+tools:
+  - legsta:
+      description: In silico Legionella pneumophila Sequence Based Typing
+      homepage: https://github.com/tseemann/legsta
+      documentation: https://github.com/tseemann/legsta
+      tool_dev_url: https://github.com/tseemann/legsta
+      doi: ""
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - seqs:
+      type: file
+      description: FASTA, GenBank or EMBL formatted files
+      pattern: "*.{fasta,gbk,embl}"
+
+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"
+  - tsv:
+      type: file
+      description: Tab-delimited summary of the results
+      pattern: "*.{tsv}"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -892,6 +892,10 @@ leehom:
   - modules/leehom/**
   - tests/modules/leehom/**
 
+legsta:
+  - modules/legsta/**
+  - tests/modules/legsta/**
+
 lima:
   - modules/lima/**
   - tests/modules/lima/**

tests/modules/legsta/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LEGSTA } from '../../../modules/legsta/main.nf'
+
+workflow test_legsta {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+    ]
+
+    LEGSTA ( input )
+}

tests/modules/legsta/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/legsta/test.yml

@@ -0,0 +1,9 @@
+- name: legsta test_legsta
+  command: nextflow run tests/modules/legsta -entry test_legsta -c tests/config/nextflow.config
+  tags:
+    - legsta
+  files:
+    - path: output/legsta/test.tsv
+      md5sum: c493bdd19335de4828aa8b4e3ce7e1f8
+    - path: output/legsta/versions.yml
+      md5sum: d16c5f6fd68d2bcc2c71954e3342aabe