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https://github.com/MillironX/nf-core_modules.git
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f3ffa69b8d
* feat(dragmap): Add initial hastable module * feat(dragmap): Add initial align module * test(dragmap): Remove md5sum Forgot sam files have a header. Might pipe this through samtools. * build(dragmap): Add mulled container * chore(dragmap): Update prefix * feat(dragmap): Output a bam file * feat(dragmap): Add log files * Update modules/dragmap/align/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
33 lines
905 B
Text
33 lines
905 B
Text
process DRAGMAP_HASHTABLE {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0':
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'quay.io/biocontainers/dragmap:1.2.1--hd4ca14e_0' }"
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input:
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path fasta
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output:
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path "dragmap" , emit: hashmap
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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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mkdir dragmap
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dragen-os \\
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--build-hash-table true \\
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--ht-reference $fasta \\
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--output-directory dragmap \\
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$args \\
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--ht-num-threads $task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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dragmap: \$(echo \$(dragen-os --version 2>&1))
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END_VERSIONS
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"""
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}
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