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https://github.com/MillironX/nf-core_modules.git
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ae92159762
* Initial structure * Working with local singularity image * Working generateMap.pl script * Remote not working bioconda * Working generateMap with biocontainer * Lint changes * Updated hmmcopy container version to be consistent * Fix failing test * Remove path to perl * No hardpath to script * Update main.nf Moved version outside of process, add support for zipped fasta file * Revert to not allowing gzip via pipe, as perl script can't cope Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
38 lines
887 B
Text
38 lines
887 B
Text
def VERSION = '0.1.1'
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process HMMCOPY_GENERATEMAP {
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tag '$bam'
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label 'process_long'
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conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
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'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
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input:
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path fasta
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output:
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path "*.map.bw" , emit: bigwig
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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"""
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# build required indexes
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generateMap.pl -b \\
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$args \\
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$fasta
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# run
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generateMap.pl \\
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$args \\
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$fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmmcopy: \$(echo $VERSION)
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END_VERSIONS
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"""
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}
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