nf-core_modules/modules/nanolyse/main.nf

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add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert 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'
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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params.options = [:]
options = initOptions(params.options)
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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process NANOLYSE {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0"
} else {
container "quay.io/biocontainers/nanolyse:1.2.0--py_0"
}
input:
tuple val(meta), path(fastq)
path fasta
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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output:
tuple val(meta), path("*.fastq.gz"), emit: fastq
path "*.log" , emit: log
path "versions.yml" , emit: versions
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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"""
gunzip -c $fastq | NanoLyse -r $fasta | gzip > ${prefix}.fastq.gz
mv NanoLyse.log ${prefix}.nanolyse.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(NanoLyse --version 2>&1 | sed -e "s/NanoLyse //g")
END_VERSIONS
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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"""
}