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ramsainanduriramsainanduri
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new module: pharmcat/reporter (nf-core#10136)
* add new module pharmcat/reporter * updated output emit channel names
1 parent a189b32 commit c75d052

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‎modules/nf-core/pharmcat/reporter/environment.yml‎

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---
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::pharmcat3=3.1.1

‎modules/nf-core/pharmcat/reporter/main.nf‎

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process PHARMCAT_REPORTER {
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tag "$meta.id"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2b27c134f2226e65c3be9687fdcd6dfb5eebb7998bf1ad89ff396c914fe6d81a/data'
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: 'community.wave.seqera.io/library/pharmcat3:3.1.1--876b7152770ba008'}"
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input:
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tuple val(meta), path(phenotypes)
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output:
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tuple val(meta), path("*.report.json") , optional: true , emit: report_json
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tuple val(meta), path("*.report.html") , optional: true , emit: report_html
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tuple val(meta), path("*.report.tsv") , optional: true , emit: report_tsv
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tuple val("${task.process}"), val('pharmcat'), eval("pharmcat --version | cut -f2 -d ' '"), topic: versions , emit: versions_pharmcat
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}.pharmcat"
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"""
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pharmcat \\
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-reporter \\
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--reporter-input ${phenotypes} \\
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--base-filename ${prefix} \\
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--output-dir . \\
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${args}
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}.pharmcat"
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"""
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echo ${args} >/dev/null
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touch ${prefix}.report.json
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touch ${prefix}.report.html
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touch ${prefix}.report.tsv
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"""
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}

‎modules/nf-core/pharmcat/reporter/meta.yml‎

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name: "pharmcat_reporter"
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description: |
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The Reporter module is responsible for generating a report with genotype-specific
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expert-reviewed drug prescribing recommendations for clinical decision support.
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keywords:
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- pharmcat
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- report
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- PGx
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tools:
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- "pharmcat":
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description: |
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"PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics
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tool that analyzes genetic variants to predict drug response and tailor medical
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treatment to an individual patient’s genetic profile."
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homepage: "https://pharmcat.clinpgx.org/"
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documentation: "https://pharmcat.clinpgx.org/"
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tool_dev_url: "https://github.com/PharmGKB/PharmCAT"
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doi: "10.1002/cpt.928"
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licence:
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- "MPL-2.0"
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'test', name:'test_sample' ]`
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- phenotypes:
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type: file
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description: The vcf file to be inspected
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pattern: "*.json"
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ontologies:
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- edam: http://edamontology.org/format_3464
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output:
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report_json:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'test', name:'test_sample' ]`
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- "*.report.json":
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type: file
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description: Json output from the reporter module of PharmCAT
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pattern: "*.report.json"
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ontologies:
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- edam: http://edamontology.org/format_3464
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report_html:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'test', name:'test_sample' ]`
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- "*.report.html":
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type: file
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description: HTML output from the reporter module of PharmCAT
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pattern: "*.report.html"
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ontologies: []
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report_tsv:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'test', name:'test_sample' ]`
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- "*.report.tsv":
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type: file
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description: Tab separated output from the reporter module of PharmCAT
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pattern: "*.report.tsv"
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ontologies: []
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versions_pharmcat:
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- - ${task.process}:
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type: string
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description: The name of the process
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- pharmcat:
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type: string
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description: The name of the tool
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- pharmcat --version | cut -f2 -d ' ':
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- pharmcat:
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type: string
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description: The name of the tool
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- pharmcat --version | cut -f2 -d ' ':
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@ramsainanduri"
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maintainers:
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- "@ramsainanduri"

‎modules/nf-core/pharmcat/reporter/tests/main.nf.test‎

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nextflow_process {
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name "Test Process PHARMCAT_REPORTER"
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script "../main.nf"
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process "PHARMCAT_REPORTER"
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tag "modules"
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tag "modules_nfcore"
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tag "pharmcat"
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tag "pharmcat/reporter"
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tag "pharmcat/phenotyper"
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tag "pharmcat/matcher"
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config "./nextflow.config"
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setup {
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run("PHARMCAT_MATCHER") {
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script "../../matcher/main.nf"
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process {
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"""
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input[0] = Channel.fromList([
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tuple([id: 'PharmCAT'], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pharmcat/test.chr22.single.sample.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/pharmcat/test.chr22.single.sample.vcf.gz.tbi', checkIfExists: true)),
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])
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input[1] = Channel.of([])
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"""
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}
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}
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run("PHARMCAT_PHENOTYPER") {
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script "../../phenotyper/main.nf"
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process {
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"""
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input[0] = PHARMCAT_MATCHER.out.matcher_json.collect {
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meta, match_json -> match_json
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}.map {
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match_json -> [
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[ id: 'test'],
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match_json,
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[]
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]
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}
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"""
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}
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}
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}
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test("report - JSON + HTML + TSV") {
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when {
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params {
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module_args = ' --reporter-save-html --reporter-save-json --reporter-save-calls-only-tsv '
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}
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process {
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"""
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input[0] = PHARMCAT_PHENOTYPER.out.phenotyper_json
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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file(process.out.report_json[0][1]).name,
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file(process.out.report_html[0][1]).name,
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file(process.out.report_tsv[0][1]).name,
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match() }
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)
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}
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}
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test("report - JSON + HTML ONLY") {
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when {
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params {
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module_args = ' --reporter-save-html --reporter-save-json '
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}
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process {
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"""
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input[0] = PHARMCAT_PHENOTYPER.out.phenotyper_json
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert process.out.report_tsv[1] == null },
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{ assert snapshot(
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file(process.out.report_json[0][1]).name,
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file(process.out.report_html[0][1]).name,
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match() }
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)
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}
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}
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test("report - JSON ONLY") {
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when {
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params {
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module_args = ' --reporter-save-json '
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}
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process {
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"""
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input[0] = PHARMCAT_PHENOTYPER.out.phenotyper_json
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert process.out.report_tsv[1] == null },
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{ assert process.out.report_html[1] == null },
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{ assert snapshot(
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file(process.out.report_json[0][1]).name,
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match() }
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)
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}
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}
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test("report - TSV ONLY") {
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when {
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params {
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module_args = ' --reporter-save-calls-only-tsv '
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}
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process {
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"""
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input[0] = PHARMCAT_PHENOTYPER.out.phenotyper_json
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert process.out.report_json[1] == null },
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{ assert process.out.report_html[1] == null },
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{ assert snapshot(
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file(process.out.report_tsv[0][1]).name,
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match() }
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)
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}
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}
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test("report - general") {
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when {
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params {
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module_args = " --reporter-sources CPIC,FDA "
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}
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process {
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"""
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input[0] = PHARMCAT_PHENOTYPER.out.phenotyper_json
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert process.out.report_json[1] == null },
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{ assert process.out.report_tsv[1] == null },
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{ assert snapshot(
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file(process.out.report_html[0][1]).name,
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process.out.findAll { key, val -> key.startsWith("versions") }
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).match() }
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)
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}
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}
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test("report - stub") {
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options "-stub"
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when {
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params {
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module_args = ' --reporter-extended '
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}
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process {
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"""
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input[0] = PHARMCAT_PHENOTYPER.out.phenotyper_json
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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sanitizeOutput(process.out)
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).match() }
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)
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}
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}
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}

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