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FriederikeHanssenFriederikeHanssen
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Adds seq2hla (nf-core#8939)
* add seq2hla * circumvent empty checksums
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‎modules/nf-core/seq2hla/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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- defaults
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dependencies:
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- bioconda::seq2hla=2.3

‎modules/nf-core/seq2hla/main.nf‎

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process SEQ2HLA {
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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/sha256/5c/5c8c9c11302a03e4f8fc9bbd0ce818e9f798e38f872c3ec099b8bb1c444185e0/data'
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: 'community.wave.seqera.io/library/seq2hla:2.3--26344ebe67dd0e8e'}"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*ClassI-class.bowtielog") , emit: class1_bowtielog
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tuple val(meta), path("*ClassI-class.expression") , emit: class1_expression
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tuple val(meta), path("*ClassI-class.HLAgenotype2digits") , emit: class1_genotype_2d
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tuple val(meta), path("*ClassI-class.HLAgenotype4digits") , emit: class1_genotype_4d
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tuple val(meta), path("*ClassI-nonclass.bowtielog") , emit: class1_nonclass_bowtielog
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tuple val(meta), path("*ClassI-nonclass.expression") , emit: class1_nonclass_expression
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tuple val(meta), path("*ClassI-nonclass.HLAgenotype2digits"), emit: class1_nonclass_genotype_2d
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tuple val(meta), path("*ClassI-nonclass.HLAgenotype4digits"), emit: class1_nonclass_genotype_4d
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tuple val(meta), path("*ClassII.bowtielog") , emit: class2_bowtielog
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tuple val(meta), path("*ClassII.expression") , emit: class2_expression
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tuple val(meta), path("*ClassII.HLAgenotype2digits") , emit: class2_genotype_2d
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tuple val(meta), path("*ClassII.HLAgenotype4digits") , emit: class2_genotype_4d
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tuple val(meta), path("*.ambiguity") , emit: ambiguity, optional: true
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
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seq2HLA \\
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-1 ${prefix}_1.fastq.gz \\
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-2 ${prefix}_2.fastq.gz \\
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-r ${prefix} \\
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-p ${task.cpus} \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seq2hla: \$(seq2HLA --version |& sed 's/seq2HLA.py //')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}-ClassI-class.HLAgenotype2digits
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touch ${prefix}-ClassII.HLAgenotype2digits
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touch ${prefix}-ClassI-class.HLAgenotype4digits
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touch ${prefix}-ClassII.HLAgenotype4digits
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touch ${prefix}-ClassI-class.bowtielog
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touch ${prefix}-ClassII.bowtielog
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touch ${prefix}-ClassI-class.expression
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touch ${prefix}-ClassII.expression
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touch ${prefix}-ClassI-nonclass.HLAgenotype2digits
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touch ${prefix}-ClassI-nonclass.HLAgenotype4digits
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touch ${prefix}-ClassI-nonclass.bowtielog
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touch ${prefix}-ClassI-nonclass.expression
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touch ${prefix}.ambiguity
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seq2hla: \$(seq2HLA --version |& sed 's/seq2HLA.py //')
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END_VERSIONS
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"""
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}

‎modules/nf-core/seq2hla/meta.yml‎

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---
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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: "seq2hla"
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description: Precision HLA typing and expression from RNA-seq data using seq2HLA
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keywords:
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- hla
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- typing
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- rna-seq
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- genomics
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- immunogenetics
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tools:
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- "seq2hla":
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description: "Precision HLA typing and expression from next-generation RNA sequencing data"
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homepage: "https://github.com/TRON-Bioinformatics/seq2HLA"
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documentation: "https://github.com/TRON-Bioinformatics/seq2HLA#readme"
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tool_dev_url: "https://github.com/TRON-Bioinformatics/seq2HLA"
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doi: "10.1186/s13073-015-0240-5"
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licence: ['MIT']
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identifier: biotools:seq2HLA
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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', single_end:false ]`
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- reads:
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type: file
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description: Paired-end FASTQ files for RNA-seq data
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pattern: "*.{fastq.gz,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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class1_genotype_2d:
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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', single_end:false ]`
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- "*ClassI-class.HLAgenotype2digits":
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type: file
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description: HLA Class I 2-digit genotype results
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pattern: "*ClassI-class.HLAgenotype2digits"
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ontologies: []
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class2_genotype_2d:
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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', single_end:false ]`
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- "*ClassII.HLAgenotype2digits":
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type: file
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description: HLA Class II 2-digit genotype results
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pattern: "*ClassII.HLAgenotype2digits"
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ontologies: []
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class1_genotype_4d:
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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', single_end:false ]`
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- "*ClassI-class.HLAgenotype4digits":
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type: file
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description: HLA Class I 4-digit genotype results
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pattern: "*ClassI-class.HLAgenotype4digits"
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ontologies: []
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class2_genotype_4d:
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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', single_end:false ]`
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- "*ClassII.HLAgenotype4digits":
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type: file
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description: HLA Class II 4-digit genotype results
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pattern: "*ClassII.HLAgenotype4digits"
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ontologies: []
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class1_bowtielog:
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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', single_end:false ]`
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- "*ClassI-class.bowtielog":
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type: file
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description: HLA Class I Bowtie alignment log
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pattern: "*ClassI-class.bowtielog"
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ontologies: []
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class2_bowtielog:
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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', single_end:false ]`
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- "*ClassII.bowtielog":
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type: file
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description: HLA Class II Bowtie alignment log
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pattern: "*ClassII.bowtielog"
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ontologies: []
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class1_expression:
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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', single_end:false ]`
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- "*ClassI-class.expression":
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type: file
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description: HLA Class I expression results
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pattern: "*ClassI-class.expression"
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ontologies: []
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class2_expression:
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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', single_end:false ]`
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- "*ClassII.expression":
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type: file
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description: HLA Class II expression results
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pattern: "*ClassII.expression"
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ontologies: []
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class1_nonclass_genotype_2d:
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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', single_end:false ]`
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- "*ClassI-nonclass.HLAgenotype2digits":
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type: file
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description: HLA Class I non-classical 2-digit genotype results
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pattern: "*ClassI-nonclass.HLAgenotype2digits"
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ontologies: []
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ambiguity:
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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', single_end:false ]`
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- "*.ambiguity":
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type: file
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description: HLA typing ambiguity results
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pattern: "*.ambiguity"
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ontologies: []
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class1_nonclass_genotype_4d:
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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', single_end:false ]`
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- "*ClassI-nonclass.HLAgenotype4digits":
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type: file
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description: HLA Class I non-classical 4-digit genotype results
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pattern: "*ClassI-nonclass.HLAgenotype4digits"
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ontologies: []
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class1_nonclass_bowtielog:
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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', single_end:false ]`
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- "*ClassI-nonclass.bowtielog":
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type: file
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description: HLA Class I non-classical Bowtie alignment log
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pattern: "*ClassI-nonclass.bowtielog"
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ontologies: []
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class1_nonclass_expression:
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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', single_end:false ]`
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- "*ClassI-nonclass.expression":
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type: file
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description: HLA Class I non-classical expression results
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pattern: "*ClassI-nonclass.expression"
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ontologies: []
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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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- "@FriederikeHanssen"
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maintainers:
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- "@FriederikeHanssen"

‎modules/nf-core/seq2hla/tests/main.nf.test‎

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nextflow_process {
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name "Test Process SEQ2HLA"
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script "../main.nf"
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process "SEQ2HLA"
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tag "modules"
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tag "modules_nfcore"
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tag "seq2hla"
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test("homo_sapiens - fastq") {
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when {
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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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[
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', 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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then {
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assert process.success
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assertAll(
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{ assert snapshot(
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process.out.class1_bowtielog,
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process.out.class1_genotype_2d,
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process.out.class1_genotype_4d,
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process.out.class1_nonclass_bowtielog,
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process.out.class1_nonclass_genotype_2d,
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process.out.class1_nonclass_genotype_4d,
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process.out.class2_bowtielog,
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process.out.class2_genotype_2d,
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process.out.class2_genotype_4d,
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process.out.ambiguity,
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process.out.versions
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).match() },
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{ assert file(process.out.class1_expression[0][1]).name.endsWith("ClassI-class.expression") },
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{ assert file(process.out.class2_expression[0][1]).name.endsWith("ClassII.expression") },
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{ assert file(process.out.class1_nonclass_expression[0][1]).name.endsWith("ClassI-nonclass.expression") }
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)
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}
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}
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test("homo_sapiens - fastq - 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] = [
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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/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', 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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then {
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assert process.success
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assertAll(
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

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