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https://github.com/MillironX/nf-core_modules.git
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01d6d4c286
* Creation of Glimpse Chunk Add sub tools chunk with configuration and needed files for unitest. * Code linting correction * Prettier ran Newline deleted in nextflow.config * New final line and white spaces * Change Pytest.yml to work as a subtool. * Control for the parameters deleted. Control for the size/count of the window and buffer not needed. They have some defaults value. * Changed the different recommended part by @nvnieuwk Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
39 lines
1.1 KiB
Text
39 lines
1.1 KiB
Text
process GLIMPSE_CHUNK {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::glimpse-bio=1.1.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2':
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'quay.io/biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
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input:
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tuple val(meta), path(input)
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val region
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output:
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tuple val(meta), path("*.txt"), emit: chunk_chr
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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 prefix = task.ext.prefix ?: "${meta.id}"
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def args = task.ext.args ?: ""
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def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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GLIMPSE_chunk \\
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$args \\
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--input $input \\
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--region $region \\
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--thread $task.cpus \\
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--output ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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glimpse: $VERSION
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END_VERSIONS
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"""
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}
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