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‎.devcontainer/devcontainer.json‎

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{
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"name": "nfcore-modules",
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"image": "nfcore/devcontainer:dev",
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"remoteEnv": {
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// Workspace path on the host for mounting with docker-outside-of-docker
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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},
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"onCreateCommand": "./.devcontainer/setup.sh",
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"remoteUser": "root",
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"privileged": true,
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"hostRequirements": {
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"cpus": 4,
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"memory": "16gb",
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"storage": "32gb"
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}
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}

‎.devcontainer/setup.sh‎

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#!/usr/bin/env bash
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# Customise the terminal command prompt
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echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
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echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
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export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
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# Update Nextflow
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nextflow self-update
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# Install pre-commit hooks
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pre-commit install --install-hooks
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# Update welcome message
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echo "Welcome to nf-core/modules devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

‎modules/nf-core/deacon/filter/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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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::deacon=0.5.0

‎modules/nf-core/deacon/filter/main.nf‎

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process DEACON_FILTER {
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tag "$meta.id"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deacon:0.5.0--h4349ce8_0':
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'biocontainers/deacon:0.5.0--h4349ce8_0' }"
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input:
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tuple val(meta), path(index), path(reads)
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output:
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tuple val(meta), path("${prefix}*.fq") , emit: fastq_filtered
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tuple val(meta), path("${prefix}.json"), emit: log
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def read_type = (reads instanceof List) ? "-o ${prefix}_1.fq -O ${prefix}_2.fq" : "> ${prefix}.fq"
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"""
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deacon \\
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filter \\
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--threads ${task.cpus} \\
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$args \\
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--summary ${prefix}.json \\
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-d $index \\
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$reads \\
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${read_type}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deacon: \$(deacon --version | head -n1 | sed 's/deacon //g')
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END_VERSIONS
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"""
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stub:
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.fq
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touch ${prefix}.json
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deacon: \$(deacon --version | head -n1 | sed 's/deacon //g')
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END_VERSIONS
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"""
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}

‎modules/nf-core/deacon/filter/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "deacon_filter"
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description: Filter DNA sequences using index of reference genome
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keywords:
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- filter
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- index
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- fasta
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- fastq
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- genome
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- reference
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- minimizer
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- decontamination
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tools:
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- "deacon":
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description: "Fast alignment-free sequence filter"
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homepage: "https://github.com/bede/deacon"
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documentation: "https://github.com/bede/deacon#readme"
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tool_dev_url: "https://github.com/bede/deacon"
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doi: "10.1093/bioinformatics/btae004"
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licence: ["MIT"]
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identifier: "biotools:deacon"
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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 reference information.
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e.g. [ id:'test', single_end:false ]
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- index:
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type: file
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description: Deacon minimizer index file
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pattern: "*.idx"
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ontologies:
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- edam: "http://edamontology.org/data_3210" # Genome index
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- reads:
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type: file
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description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
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pattern: "*.{fastq,fastq.gz,fqs,fqs.gz,fq,fq.gz}"
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ontologies:
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- edam: "http://edamontology.org/format_1930" # FASTQ
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output:
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fastq_filtered:
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- - meta:
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type: map
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description: |
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Groovy Map containing reference information.
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e.g. [ id:'test', single_end:false ]
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- "${prefix}*.fq":
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type: file
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description: List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
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pattern: "*.fq"
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ontologies:
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- edam: "http://edamontology.org/format_1930" # FASTQ
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log:
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- - meta:
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type: map
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description: |
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Groovy Map containing reference information.
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e.g. [ id:'test', single_end:false ]
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- "${prefix}.json":
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type: file
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description: JSON file containing summary of results.
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pattern: "*.json"
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ontologies:
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- edam: "http://edamontology.org/format_3464" # JSON
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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authors:
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- "@Baksic-Ivan"
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- "@Omer0191"
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maintainers:
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- "@Baksic-Ivan"
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- "@Omer0191"
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- "@vagkaratzas"

‎modules/nf-core/deacon/filter/tests/main.nf.test‎

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nextflow_process {
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name "Test Process DEACON_FILTER"
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script "../main.nf"
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process "DEACON_FILTER"
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tag "modules"
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tag "modules_nfcore"
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tag "deacon"
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tag "deacon/filter"
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tag "deacon/index"
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test("sarscov2 - fastq - single-end") {
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setup {
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run("DEACON_INDEX") {
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script "../../index/main.nf"
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process {
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"""
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input[0] = [
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[ id:'test', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
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]
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"""
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}
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}
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}
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when {
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process {
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"""
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filter_fastq_ch = Channel.of(
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[
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[ id:'test', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
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]
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)
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input[0] = DEACON_INDEX.out.index.join(filter_fastq_ch)
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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.log[0][1]).name,
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process.out.fastq_filtered,
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process.out.versions.collect { path(it).yaml }
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).match()}
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)
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}
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}
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test("sarscov2 - fastq - paired-end") {
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setup {
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run("DEACON_INDEX") {
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script "../../index/main.nf"
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process {
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"""
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input[0] = [
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[ id:'test', single_end:false ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
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]
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"""
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}
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}
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}
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when {
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process {
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"""
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filter_fastq_ch = Channel.of(
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[
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[ id:'test', single_end:false ], // meta map
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[
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
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]
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]
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)
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input[0] = DEACON_INDEX.out.index.join(filter_fastq_ch)
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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.log[0][1]).name,
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process.out.fastq_filtered
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).match()},
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{ assert snapshot(process.out.versions).match("versions") }
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)
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}
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}
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test("sarscov2 - fastq - single-end - stub") {
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options "-stub"
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setup {
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run("DEACON_INDEX") {
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script "../../index/main.nf"
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process {
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"""
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input[0] = [
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[ id:'test', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
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]
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"""
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}
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}
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}
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when {
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process {
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"""
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filter_fastq_ch = Channel.of(
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[
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[ id:'test', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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]
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)
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input[0] = DEACON_INDEX.out.index.join(filter_fastq_ch)
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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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process.out,
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process.out.versions.collect { path(it).yaml }
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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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