Islandpath (#3145)

* chore: Init module boilerplate

* feat: Build initial version of islandpath module

* test: Update islandpath test

* chore: Remove comment

* test: Add contains

* fix: Change identation

* Apply suggestions from code review

Co-authored-by: Louisa Perelo <[email protected]>

* Add islandpath to conda exclude in the CI

* Capitalize log in meta.yml

* [automated] Fix linting with Prettier

* lint: Fix doi

---------

Co-authored-by: Louisa Perelo <[email protected]>
Co-authored-by: nf-core-bot <[email protected]>

.github/workflows/pytest-workflow.yml

@@ -136,7 +136,8 @@ jobs:
             tags: subworkflows/bcl_demultiplex
           - profile: "conda"
             tags: subworkflows/vcf_annotate_ensemblvep
-
+          - profile: "conda"
+            tags: islandpath
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

modules/nf-core/islandpath/main.nf

@@ -0,0 +1,37 @@
+process ISLANDPATH {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::islandpath=1.0.6"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/islandpath:1.0.6--hdfd78af_0':
+        'quay.io/biocontainers/islandpath:1.0.6--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(genome)
+
+    output:
+    tuple val(meta), path("*.gff")        , emit: gff
+    path "Dimob.log"                      , emit: log
+    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}"
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.0.6'
+    """
+    islandpath \\
+        $genome \\
+        ${prefix}.gff \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        islandpath: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/islandpath/meta.yml

@@ -0,0 +1,44 @@
+name: islandpath
+description: Genomic island prediction in bacterial and archaeal genomes
+keywords:
+  - genomes
+  - genomic islands
+  - prediction
+tools:
+  - "islandpath":
+      description: "IslandPath-DIMOB is a standalone software to predict genomic islands (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes."
+      homepage: https://github.com/brinkmanlab/islandpath
+      documentation: https://github.com/brinkmanlab/islandpath#readme
+      tool_dev_url: https://github.com/brinkmanlab/islandpath
+      doi: "10.1093/bioinformatics/bty095"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - genome:
+      type: file
+      description: |
+        Genome file in .gbk or .embl format.
+        pattern: "*.{gbk, embl, gbff}"
+
+output:
+  - gff:
+      type: file
+      description: GFF file listing the predicted genomic islands and their coordinates
+      pattern: "*.gff"
+  - log:
+      type: file
+      description: Log file of the islandpath run
+      pattern: "*.log"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@jvfe"

tests/config/pytest_modules.yml

@@ -1837,6 +1837,10 @@ iqtree:
   - modules/nf-core/iqtree/**
   - tests/modules/nf-core/iqtree/**
 
+islandpath:
+  - modules/nf-core/islandpath/**
+  - tests/modules/nf-core/islandpath/**
+
 ismapper:
   - modules/nf-core/ismapper/**
   - tests/modules/nf-core/ismapper/**

tests/modules/nf-core/islandpath/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP } from '../../../../modules/nf-core/gunzip/main.nf'
+include { ISLANDPATH } from '../../../../modules/nf-core/islandpath/main.nf'
+
+workflow test_islandpath {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+
+    ISLANDPATH ( GUNZIP.out.gunzip )
+}

tests/modules/nf-core/islandpath/nextflow.config

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

tests/modules/nf-core/islandpath/test.yml

@@ -0,0 +1,11 @@
+- name: islandpath test_islandpath
+  command: nextflow run ./tests/modules/nf-core/islandpath -entry test_islandpath -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/islandpath/nextflow.config
+  tags:
+    - islandpath
+  files:
+    - path: output/islandpath/Dimob.log
+      contains:
+        - "Running IslandPath-DIMOB"
+    - path: output/islandpath/test.gff
+      md5sum: d4719f73e9af606346fade238aa191fa
+    - path: output/islandpath/versions.yml