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90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
process AMPIR {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
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container "${ 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 model
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val min_length
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val min_probability
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output:
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tuple val(meta), path("*.faa"), emit: amps_faa
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tuple val(meta), path("*.tsv"), emit: amps_tsv
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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 ?: "${meta.id}"
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min_length = ("${min_length}" == "[]") ? "": " min_len = as.integer(${min_length})," // Fall back to AMPir default value if none specified
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if ("$faa" == "${prefix}.faa") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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"""
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#!/usr/bin/env Rscript
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library(ampir)
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input_seqs <- read_faa('${faa}')
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prediction <- predict_amps(input_seqs,${min_length} model = '${model}')
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prediction <- prediction[which(prediction\$prob_AMP >= as.numeric(${min_probability})), ]
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output_seqs <- input_seqs[row.names(prediction), ]
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write.table(prediction, file = "${prefix}.tsv", row.names = FALSE, sep = "\t", quote = FALSE, dec = '.')
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df_to_faa(output_seqs, "${prefix}.faa")
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version_file_path <- "versions.yml"
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version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
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f <- file(version_file_path, "w")
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writeLines('"${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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