add module for pbptyper (#2005)

* add module for pbptyper

* add optional database parameter

modules/pbptyper/main.nf

@@ -0,0 +1,38 @@
+process PBPTYPER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::pbptyper=1.0.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pbptyper:1.0.2--hdfd78af_0':
+        'quay.io/biocontainers/pbptyper:1.0.2--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path(db)
+
+    output:
+    tuple val(meta), path("${prefix}.tsv"), emit: tsv
+    tuple val(meta), path("*.tblastn.tsv"), emit: blast
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def db_args = db ? '--db ${db}' : ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    pbptyper \\
+        $db_args \\
+        $args \\
+        --prefix $prefix \\
+        --assembly $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbptyper: \$(echo \$(pbptyper --version 2>&1) | sed 's/^.*pbptyper, version //;' )
+    END_VERSIONS
+    """
+}

modules/pbptyper/meta.yml

@@ -0,0 +1,52 @@
+name: "pbptyper"
+description: Assign PBP type of Streptococcus pneumoniae assemblies
+keywords:
+  - bacteria
+  - pbp
+  - fasta
+  - assembly
+tools:
+  - "pbptyper":
+      description: "In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies"
+      homepage: "https://github.com/rpetit3/pbptyper"
+      documentation: "https://github.com/rpetit3/pbptyper"
+      tool_dev_url: "https://github.com/rpetit3/pbptyper"
+      doi: ""
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: An assembly in FASTA format
+      pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}"
+  - db:
+      type: file
+      description: A reference PBP database (optional)
+      pattern: "*.{fasta,fna,fa}"
+
+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: A tab-delimited file with the predicted PBP type
+      pattern: "*.tsv"
+  - blast:
+      type: file
+      description: A tab-delimited file of all blast hits
+      pattern: "*.tblastn.tsv"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -1723,6 +1723,10 @@ pbccs:
   - modules/pbccs/**
   - tests/modules/pbccs/**
 
+pbptyper:
+  - modules/pbptyper/**
+  - tests/modules/pbptyper/**
+
 pear:
   - modules/pear/**
   - tests/modules/pear/**

tests/modules/pbptyper/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PBPTYPER } from '../../../modules/pbptyper/main.nf'
+
+workflow test_pbptyper {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PBPTYPER ( input, [] )
+}

tests/modules/pbptyper/nextflow.config

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

tests/modules/pbptyper/test.yml

@@ -0,0 +1,13 @@
+- name: pbptyper test_pbptyper
+  command: nextflow run ./tests/modules/pbptyper -entry test_pbptyper -c ./tests/config/nextflow.config  -c ./tests/modules/pbptyper/nextflow.config
+  tags:
+    - pbptyper
+  files:
+    - path: output/pbptyper/test-1A.tblastn.tsv
+      md5sum: 16bb26284bd7bf2327337fc95c055429
+    - path: output/pbptyper/test-2B.tblastn.tsv
+      md5sum: 16bb26284bd7bf2327337fc95c055429
+    - path: output/pbptyper/test-2X.tblastn.tsv
+      md5sum: 16bb26284bd7bf2327337fc95c055429
+    - path: output/pbptyper/test.tsv
+      md5sum: 7115fb3533ee30f0a7dde61a42f69185