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Feature/localcdsearch (#9632)
* local-cd-search annotate and download modules * Fixing lint * Update localcdsearch tool metadata in meta.yml * Fix container URL selection logic in main.nf * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Update modules/nf-core/localcdsearch/annotate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Singularity container added * edamontology added * Updating test for one input only * Updating snap * Updating test for db downloding * Update version handling in main.nf * Update version expression in meta.yml * Refactor version handling in main.nf Updated version information to use a variable for better maintainability. * Update version retrieval expression in meta.yml * Add version information to stub Added version information for the tool in the main.nf file. * Add version information to stub Added version information to the main.nf file. * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> * Refactor assertions to include process success check * Refactor assertions for process success in tests * Update container URL for local-cd-search * Remove redundant success assertion in tests --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
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‎modules/nf-core/localcdsearch/annotate/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::local-cd-search=0.3.0"

‎modules/nf-core/localcdsearch/annotate/main.nf‎

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process LOCALCDSEARCH_ANNOTATE {
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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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e1/e1ed921c933d8eeeb0db6d72ece09ec25edab9ad441c84b070acff1592af2d54/data' :
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'biocontainers/local-cd-search:0.3.0--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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path db
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val sites
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output:
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tuple val(meta), path("*_results.tsv"), emit: result
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tuple val(meta), path("*_sites.tsv") , emit: annot_sites, optional: true
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tuple val("${task.process}"), val('local-cd-search'), eval("echo ${VERSION}"), topic: versions, emit: versions_localcdsearch
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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VERSION = '0.3.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def prefix = task.ext.prefix ?: "${meta.id}"
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def val_flag = sites ? "--sites-output ${prefix}_sites.tsv" : ''
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def is_compressed = fasta.getExtension() == "gz"
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def fasta_name = is_compressed ? fasta.getBaseName() : fasta
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def uncompress_input = is_compressed ? "gzip -c -d ${fasta} > ${fasta_name}" : ''
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"""
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$uncompress_input
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local-cd-search \\
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annotate \\
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$args \\
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$val_flag \\
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--threads $task.cpus \\
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${fasta_name} \\
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${prefix}_results.tsv \\
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${db}
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"""
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stub:
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def args = task.ext.args ?: ''
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VERSION = '0.3.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo $args
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touch ${prefix}_results.tsv
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${sites ? "touch ${prefix}_sites.tsv" : ''}
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"""
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}

‎modules/nf-core/localcdsearch/annotate/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: "localcdsearch_annotate"
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description: A command-line tool for local protein domain annotation using NCBI's Conserved Domain Database (CDD)
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keywords:
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- cdd
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- rpsblast
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- rpsbproc
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- protein
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- domain
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- annotation
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tools:
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- "localcdsearch":
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description: "Protein annotation using local PSSM databases from CDD."
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homepage: "https://github.com/apcamargo/local-cd-search"
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documentation: "https://github.com/apcamargo/local-cd-search"
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tool_dev_url: "https://github.com/apcamargo/local-cd-search"
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licence: ["MIT"]
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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:'sample1' ]`
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- fasta:
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type: file
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description: Input fasta file containing protein queries sequences
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pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
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ontologies:
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- edam: "http://edamontology.org/format_1929" # FASTA
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- db:
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type: directory
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description: Directory containing the metadata and databse directories
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pattern: "*"
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- sites:
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type: boolean
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description: When true an extra tsv output file is generated
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output:
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result:
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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:'sample1' ]`
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- "*_results.tsv":
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type: file
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description: tab-separated file with hits filtered by CDD's curated bit-score thresholds
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pattern: "*_results.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475 # TSV
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annot_sites:
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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:'sample1' ]`
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- "*_sites.tsv":
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type: file
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description: If --sites-output is specified, an additional tab-separated file is created with functional site annotations
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pattern: "*_sites.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475 # TSV
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versions_localcdsearch:
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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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- "local-cd-search":
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type: string
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description: The name of the tool
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- "echo ${VERSION}":
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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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- local-cd-search:
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type: string
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description: The name of the tool
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- echo ${VERSION}:
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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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- "@Ales-ibt"
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maintainers:
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- "@Ales-ibt"

‎modules/nf-core/localcdsearch/annotate/tests/main.nf.test‎

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nextflow_process {
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name "Test Process LOCALCDSEARCH_ANNOTATE"
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script "../main.nf"
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process "LOCALCDSEARCH_ANNOTATE"
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tag "modules"
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tag "modules_nfcore"
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tag "localcdsearch"
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tag "localcdsearch/annotate"
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tag "localcdsearch/download"
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setup {
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run("LOCALCDSEARCH_DOWNLOAD") {
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script "../../download/main.nf"
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process {
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"""
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input[0] = ['smart']
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"""
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}
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}
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}
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test("sarscov2 - smart") {
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when {
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process {
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"""
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input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
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input[1] = LOCALCDSEARCH_DOWNLOAD.out.db
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input[2] = false
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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.result,
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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("sarscov2 - smart - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
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input[1] = LOCALCDSEARCH_DOWNLOAD.out.db
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input[2] = false
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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.result,
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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("sarscov2 - smart - sites") {
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when {
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process {
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"""
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input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
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input[1] = LOCALCDSEARCH_DOWNLOAD.out.db
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input[2] = true
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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.result,
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process.out.annot_sites,
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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("sarscov2 - smart - sites - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
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input[1] = LOCALCDSEARCH_DOWNLOAD.out.db
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input[2] = true
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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.result,
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process.out.annot_sites,
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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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}

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