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a8b0fce8ce
* adding tailfindr module * replacing the container * removing todo * removing todo and fixing meta.yml * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/tailfindr/test.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update main.nf * Update meta.yml * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update meta.yml * Update main.nf * adding pytest * Update main.nf * Update modules/tailfindr/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update test.yml * Update main.nf * Update main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
38 lines
1.3 KiB
Text
38 lines
1.3 KiB
Text
process TAILFINDR {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::ont-fast5-api=0.4.1 bioconda::r-tailfindr=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0':
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'quay.io/biocontainers/mulled-v2-f24f1399a77784f913670cbb36a0f17b78e0631b:80e40d512cd5a71665e3e00e8d0ad1462fc58f76-0' }"
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input:
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tuple val(meta), path(fast5)
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output:
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tuple val(meta), path("*.csv.gz"), emit: csv_gz
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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 ? ", ${task.ext.args}": ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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R --vanilla --slave -e "library(tailfindr);
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find_tails(fast5_dir = './' ,
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save_dir = './' ${args},
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csv_filename = \'${meta.id}.csv\',
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num_cores = ${task.cpus})";
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gzip ${meta.id}.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tailfindr: \$(Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))")
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ont-fast5-api: \$(pip show ont-fast5-api | grep Version | awk '{print \$2}')
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END_VERSIONS
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"""
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}
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