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https://github.com/MillironX/nf-core_modules.git
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37c6d4a1a1
* first commit
* single taxon input
* added .tsv output
* input: single taxon or file with taxon identifiers
* updated input and output
* removed wrong tool description
* added tests
* ext.args = '-l -b'
* fixed wrong input names
* updated test file
* Update modules/goat/taxonsearch/main.nf
simple version output
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* removed 'NO_FILE' from input definition
* added ! in if statement
* optional input: empty list
* successful updated test
* added test with file
* remove blank spaces in include {}
* added test with taxa file
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
process GOAT_TAXONSEARCH {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::goat=0.2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0':
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'quay.io/biocontainers/goat:0.2.0--h92d785c_0' }"
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input:
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tuple val(meta), val(taxon), path(taxa_file)
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output:
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tuple val(meta), path("*.tsv"), emit: taxonsearch
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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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input = taxa_file ? "-f ${taxa_file}" : "-t ${taxon}"
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if (!taxon && !taxa_file) error "No input. Valid input: single taxon identifier or a .txt file with identifiers"
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if (taxon && taxa_file ) error "Only one input is required: a single taxon identifier or a .txt file with identifiers"
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"""
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goat-cli taxon search \\
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$args \\
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$input > ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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goat: \$(goat-cli --version | cut -d' ' -f2)
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END_VERSIONS
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"""
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}
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