Merge branch 'master' into update-panaroo/run

* master:
  New module : Pilon (nf-core#3331)
  Islandpath (nf-core#3145)

.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"

modules/nf-core/pilon/main.nf

@@ -0,0 +1,43 @@
+process PILON {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::pilon=1.24"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pilon:1.24--hdfd78af_0':
+        'quay.io/biocontainers/pilon:1.24--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    tuple val(meta_bam), path(bam), path(bai)
+    val pilon_mode
+
+    output:
+    tuple val(meta), path("*.fasta") , emit: improved_assembly
+    tuple val(meta), path("*.vcf")   , emit: vcf               , optional : true
+    tuple val(meta), path("*.change"), emit: change_record     , optional : true
+    tuple val(meta), path("*.bed")   , emit: tracks_bed        , optional : true
+    tuple val(meta), path("*.wig")   , emit: tracks_wig        , optional : true
+    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}"
+    def valid_mode = ["frags", "jumps", "unpaired", "bam"]
+    if ( !valid_mode.contains(pilon_mode) )  { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
+    """
+    pilon \\
+        --genome $fasta \\
+        --output ${meta.id} \\
+        --threads $task.cpus \\
+        $args \\
+        --$pilon_mode $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
+    """
+}

modules/nf-core/pilon/meta.yml

@@ -0,0 +1,71 @@
+name: "pilon"
+description: Automatically improve draft assemblies and find variation among strains, including large event detection
+keywords:
+  - polishing
+  - assembly
+  - variant calling
+tools:
+  - "pilon":
+      description: "Pilon is an automated genome assembly improvement and variant detection tool."
+      homepage: "https://github.com/broadinstitute/pilon/wiki"
+      documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage"
+      tool_dev_url: "https://github.com/broadinstitute/pilon"
+      doi: "https://doi.org/10.1371/journal.pone.0112963"
+      licence: "['GPL v2']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA of the input genome
+      pattern: "*.{fasta}"
+  - bam:
+      type: file
+      description: BAM file of reads aligned to the input genome
+      pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: BAI file (BAM index) of BAM reads aligned to the input genome
+      pattern: "*.{bai}"
+  - pilon_mode:
+      type: value
+      description: Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).
+      pattern: ["frags", "jumps", "unpaired", "bam"]
+
+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"
+  - improved_assembly:
+      type: file
+      description: fasta file, improved assembly
+      pattern: "*.{fasta}"
+  - change_record:
+      type: file
+      description: file containing a space-delimited record of every change made in the assembly as instructed by the --fix option
+      pattern: "*.{change}"
+  - vcf:
+      type: file
+      description: Pilon variant output
+      pattern: "*.{vcf}"
+  - tracks_bed:
+      type: file
+      description: files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats
+      pattern: "*.{bed}"
+  - tracks_wig:
+      type: file
+      description: files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats
+      pattern: "*.{wig}"
+
+authors:
+  - "@scorreard"

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/**
@@ -2599,6 +2603,10 @@ picard/sortvcf:
   - modules/nf-core/picard/sortvcf/**
   - tests/modules/nf-core/picard/sortvcf/**
 
+pilon:
+  - modules/nf-core/pilon/**
+  - tests/modules/nf-core/pilon/**
+
 pindel/pindel:
   - modules/nf-core/pindel/pindel/**
   - tests/modules/nf-core/pindel/pindel/**

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

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

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PILON } from '../../../../modules/nf-core/pilon/main.nf'
+
+workflow test_pilon {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // meta map
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                                ])
+
+    PILON ( input, bam_tuple_ch, "bam" )
+}

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

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

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

@@ -0,0 +1,8 @@
+- name: pilon test_pilon
+  command: nextflow run ./tests/modules/nf-core/pilon -entry test_pilon -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pilon/nextflow.config
+  tags:
+    - pilon
+  files:
+    - path: output/pilon/test.fasta
+      md5sum: 2e881994820a5a641da9ea594ab4958f
+    - path: output/pilon/versions.yml