nf-core_modules/modules/diamond/makedb/main.nf

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Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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params.options = [:]
options = initOptions(params.options)
process DIAMOND_MAKEDB {
tag "$fasta"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
// Dimaond is limited to v2.0.9 because there is not a
// singularity version higher than this at the current time.
conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0'
} else {
container 'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0'
}
input:
path fasta
output:
path "${fasta}.dmnd", emit: db
path "versions.yml" , emit: versions
Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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script:
"""
diamond \\
makedb \\
--threads $task.cpus \\
--in $fasta \\
-d $fasta \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
END_VERSIONS
Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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"""
}