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43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process AMPIR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0':
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'quay.io/biocontainers/r-ampir:1.1.0' }"
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input:
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tuple val(meta), path(faa)
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val cut_off
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val model
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val output_name
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output:
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tuple val(meta), path(output_name) , emit: amps
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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 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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#!/usr/bin/env Rscript
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library(ampir)
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protein_seqs <- read_faa("${faa}")
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prediction <- predict_amps(protein_seqs, model = '$model')
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prediction <- protein_seqs[which(prediction\$prob_AMP >= as.integer($cut_off)), ]
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df_to_faa(protein_seqs, '$output_name')
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version_file_path <- "versions.yml"
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version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
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f <- file(version_file_path, "w")
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writeLines('"${task.process}":', f)
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writeLines(" ampir: ", f, sep = "")
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writeLines(version_ampir, f)
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close(f)
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"""
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}
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