add module for seroba (#1816)

* add module for seroba

* fix lint

* Update modules/seroba/run/meta.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update modules/seroba/run/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

modules/seroba/run/main.nf

@@ -0,0 +1,39 @@
+process SEROBA_RUN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::seroba=1.0.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seroba:1.0.2--pyhdfd78af_1':
+        'quay.io/biocontainers/seroba:1.0.2--pyhdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}.tsv")                              , emit: tsv
+    tuple val(meta), path("${prefix}/detailed_serogroup_info.txt"), optional: true, emit: txt
+    path "versions.yml"                                                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seroba \\
+        runSerotyping \\
+        $reads \\
+        $prefix \\
+        $args
+
+    # Avoid name collisions
+    mv ${prefix}/pred.tsv ${prefix}/${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seroba: \$(seroba version)
+    END_VERSIONS
+    """
+}

modules/seroba/run/meta.yml

@@ -0,0 +1,47 @@
+name: "seroba_run"
+description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
+keywords:
+  - fastq
+  - serotype
+  - Streptococcus pneumoniae
+tools:
+  - "seroba":
+      description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references."
+      homepage: "https://sanger-pathogens.github.io/seroba/"
+      documentation: "https://sanger-pathogens.github.io/seroba/"
+      tool_dev_url: "https://github.com/sanger-pathogens/seroba"
+      doi: "10.1099/mgen.0.000186"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: Input Illunina paired-end FASTQ files
+      pattern: "*.{fq.gz,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
+      pattern: "versions.yml"
+  - tsv:
+      type: file
+      description: The predicted serotype in tab-delimited format
+      pattern: "*.tsv"
+  - txt:
+      type: file
+      description: A detailed description of the predicted serotype
+      pattern: "*.txt"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -2183,6 +2183,10 @@ seqwish/induce:
   - modules/seqwish/induce/**
   - tests/modules/seqwish/induce/**
 
+seroba/run:
+  - modules/seroba/run/**
+  - tests/modules/seroba/run/**
+
 sexdeterrmine:
   - modules/sexdeterrmine/**
   - tests/modules/sexdeterrmine/**

tests/modules/seroba/run/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEROBA_RUN } from '../../../../modules/seroba/run/main.nf'
+
+workflow test_seroba_run {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
+                file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
+            ]
+
+    SEROBA_RUN ( input )
+}

tests/modules/seroba/run/nextflow.config

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

tests/modules/seroba/run/test.yml

@@ -0,0 +1,8 @@
+- name: seroba run test_seroba_run
+  command: nextflow run ./tests/modules/seroba/run -entry test_seroba_run -c ./tests/config/nextflow.config  -c ./tests/modules/seroba/run/nextflow.config
+  tags:
+    - seroba
+    - seroba/run
+  files:
+    - path: output/seroba/test/test.tsv
+      md5sum: 28b2ce33df270172e6a39db4429e684b