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65 lines
3.4 KiB
Text
65 lines
3.4 KiB
Text
process HMTNOTE {
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tag "$meta.id"
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label 'process_low'
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// TODO nf-core: List required Conda package(s).
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// Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
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// For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
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// TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
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conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
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'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }"
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input:
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// TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
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// MUST be provided as an input via a Groovy Map called "meta".
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// This information may not be required in some instances e.g. indexing reference genome files:
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// https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
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// TODO nf-core: Where applicable please provide/convert compressed files as input/output
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// e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
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tuple val(meta), path(vcf)
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output:
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// TODO nf-core: Named file extensions MUST be emitted for ALL output channels
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tuple val(meta), path("*_annotated.vcf"), emit: vcf
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// TODO nf-core: List additional required output channels/values here
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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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// TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
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// If the software is unable to output a version number on the command-line then it can be manually specified
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// e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
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// Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
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// TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
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// TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
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// using the Nextflow "task" variable e.g. "--threads $task.cpus"
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// TODO nf-core: Please replace the example samtools command below with your module's command
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// TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
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"""
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hmtnote \\
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annotate \\
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$vcf \\
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${prefix}_annotated.vcf \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_annotated.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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