mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
process AMPIR {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0':
|
|
'quay.io/biocontainers/r-ampir:1.1.0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(faa)
|
|
val model
|
|
val min_length
|
|
val min_probability
|
|
|
|
output:
|
|
tuple val(meta), path("*.faa"), emit: amps_faa
|
|
tuple val(meta), path("*.tsv"), emit: amps_csv
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
min_length = ("${min_length}" == "[]") ? "": " min_len = as.integer(${min_length})," // Fall back to AMPir default value if none specified
|
|
if ("$faa" == "${prefix}.faa") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
|
|
"""
|
|
#!/usr/bin/env Rscript
|
|
library(ampir)
|
|
|
|
input_seqs <- read_faa('${faa}')
|
|
prediction <- predict_amps(input_seqs,${min_length} model = '${model}')
|
|
prediction <- prediction[which(prediction\$prob_AMP >= as.numeric(${min_probability})), ]
|
|
output_seqs <- input_seqs[row.names(prediction), ]
|
|
write.table(prediction, file = "${prefix}.tsv", row.names = FALSE, sep = "\t", quote = FALSE, dec = '.')
|
|
df_to_faa(output_seqs, "${prefix}.faa")
|
|
|
|
version_file_path <- "versions.yml"
|
|
version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
|
|
f <- file(version_file_path, "w")
|
|
writeLines('"${task.process}":', f)
|
|
writeLines(" ampir: ", f, sep = "")
|
|
writeLines(version_ampir, f)
|
|
close(f)
|
|
"""
|
|
}
|