add module for mykrobe predict and genotyphi parse (#1818)

* add module for mykrobe predict and genotyphi parse

* Update meta.yml

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

modules/genotyphi/parse/main.nf

@@ -0,0 +1,33 @@
+process GENOTYPHI_PARSE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::genotyphi=1.9.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/genotyphi:1.9.1--hdfd78af_1':
+        'quay.io/biocontainers/genotyphi:1.9.1--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(json)
+
+    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}"
+    """
+    parse_typhi_mykrobe.py \\
+        --jsons $json \\
+        --prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        genotyphi: \$(echo \$(genotyphi --version 2>&1) | sed 's/^.*GenoTyphi v//;' )
+    END_VERSIONS
+    """
+}

modules/genotyphi/parse/meta.yml

@@ -0,0 +1,42 @@
+name: "genotyphi_parse"
+description: Genotype Salmonella Typhi from Mykrobe results
+keywords:
+  - genotype
+  - Salmonella Typhi
+tools:
+  - "genotyphi":
+      description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)"
+      homepage: "https://github.com/katholt/genotyphi"
+      documentation: "https://github.com/katholt/genotyphi"
+      tool_dev_url: "https://github.com/katholt/genotyphi"
+      doi: "https://github.com/katholt/genotyphi"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - json:
+      type: file
+      description: JSON formatted file of Mykrobe results
+      pattern: "*.json"
+
+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 of predicted genotypes
+      pattern: "*.tsv"
+
+authors:
+  - "@rpetit3"

modules/mykrobe/predict/main.nf

@@ -0,0 +1,41 @@
+process MYKROBE_PREDICT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1':
+        'quay.io/biocontainers/mykrobe:0.11.0--py39h2add14b_1' }"
+
+    input:
+    tuple val(meta), path(seqs)
+    val species
+
+    output:
+    tuple val(meta), path("${prefix}.csv") , emit: csv
+    tuple val(meta), path("${prefix}.json"), emit: json
+    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}"
+    """
+    mykrobe \\
+        predict \\
+        $args \\
+        --species $species \\
+        --threads $task.cpus \\
+        --sample $prefix \\
+        --format json_and_csv \\
+        --output ${prefix} \\
+        --seq $seqs
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mykrobe: \$(echo \$(mykrobe --version 2>&1) | sed 's/^.*mykrobe v//' )
+    END_VERSIONS
+    """
+}

modules/mykrobe/predict/meta.yml

@@ -0,0 +1,51 @@
+name: "mykrobe_predict"
+description: AMR predictions for supported species
+keywords:
+  - fastq
+  - bam
+  - antimicrobial resistance
+tools:
+  - "mykrobe":
+      description: "Antibiotic resistance prediction in minutes"
+      homepage: "http://www.mykrobe.com/"
+      documentation: "https://github.com/Mykrobe-tools/mykrobe/wiki"
+      tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe"
+      doi: "10.1038/ncomms10063"
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - seqs:
+      type: file
+      description: BAM or FASTQ file
+      pattern: "*.{bam,fastq.gz,fq.gz}"
+  - species:
+      type: string
+      description: Species to make AMR prediction against
+      pattern: "*"
+
+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"
+  - csv:
+      type: file
+      description: AMR predictions in CSV format
+      pattern: "*.csv"
+  - json:
+      type: file
+      description: AMR predictions in JSON format
+      pattern: "*.json"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -1063,6 +1063,10 @@ genomescope2:
   - modules/genomescope2/**
   - tests/modules/genomescope2/**
 
+genotyphi/parse:
+  - modules/genotyphi/parse/**
+  - tests/modules/genotyphi/parse/**
+
 genrich:
   - modules/genrich/**
   - tests/modules/genrich/**
@@ -1675,6 +1679,10 @@ muscle:
   - modules/muscle/**
   - tests/modules/muscle/**
 
+mykrobe/predict:
+  - modules/mykrobe/predict/**
+  - tests/modules/mykrobe/predict/**
+
 nanolyse:
   - modules/nanolyse/**
   - tests/modules/nanolyse/**

tests/modules/genotyphi/parse/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf'
+include { GENOTYPHI_PARSE } from '../../../../modules/genotyphi/parse/main.nf'
+
+workflow test_mykrobe_predict {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    MYKROBE_PREDICT ( input, "typhi" )
+    GENOTYPHI_PARSE ( MYKROBE_PREDICT.out.json )
+}

tests/modules/genotyphi/parse/nextflow.config

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

tests/modules/genotyphi/parse/test.yml

@@ -0,0 +1,12 @@
+- name: genotyphi parse test_mykrobe_predict
+  command: nextflow run ./tests/modules/genotyphi/parse -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/genotyphi/parse/nextflow.config
+  tags:
+    - genotyphi/parse
+    - genotyphi
+  files:
+    - path: output/genotyphi/test_predictResults.tsv
+      contains: ["genome", "confidence", "supported", "test", "NA"]
+    - path: output/mykrobe/test.csv
+      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
+    - path: output/mykrobe/test.json
+      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]

tests/modules/mykrobe/predict/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MYKROBE_PREDICT } from '../../../../modules/mykrobe/predict/main.nf'
+
+workflow test_mykrobe_predict {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    MYKROBE_PREDICT ( input, "typhi" )
+}

tests/modules/mykrobe/predict/nextflow.config

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

tests/modules/mykrobe/predict/test.yml

@@ -0,0 +1,10 @@
+- name: mykrobe predict test_mykrobe_predict
+  command: nextflow run ./tests/modules/mykrobe/predict -entry test_mykrobe_predict -c ./tests/config/nextflow.config  -c ./tests/modules/mykrobe/predict/nextflow.config
+  tags:
+    - mykrobe/predict
+    - mykrobe
+  files:
+    - path: output/mykrobe/test.csv
+      contains: ["susceptibility", "genotype_model", "variants", "test.paired_end.bam"]
+    - path: output/mykrobe/test.json
+      contains: ["susceptibility", "kmer_count", "files", "test.paired_end.bam"]