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Implement suggestions from code review
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parent
5a94794793
commit
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4 changed files with 22 additions and 21 deletions
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@ -11,10 +11,10 @@ process AMPIR {
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tuple val(meta), path(faa)
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tuple val(meta), path(faa)
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val cut_off
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val cut_off
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val model
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val model
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val output_name
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output:
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output:
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tuple val(meta), path(output_name) , emit: amps
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tuple val(meta), path("*.faa"), emit: amps_faa
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tuple val(meta), path("*.csv"), emit: amps_csv
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path "versions.yml" , emit: versions
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path "versions.yml" , emit: versions
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when:
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when:
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@ -27,10 +27,11 @@ process AMPIR {
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#!/usr/bin/env Rscript
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#!/usr/bin/env Rscript
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library(ampir)
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library(ampir)
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protein_seqs <- read_faa("${faa}")
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protein_seqs <- read_faa('${faa}')
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prediction <- predict_amps(protein_seqs, model = '$model')
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prediction <- predict_amps(protein_seqs, model = '${model}')
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prediction <- protein_seqs[which(prediction\$prob_AMP >= as.integer($cut_off)), ]
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prediction <- protein_seqs[which(prediction\$prob_AMP >= as.integer(${cut_off})), ]
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df_to_faa(protein_seqs, '$output_name')
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df_to_faa(protein_seqs, "${prefix}.faa")
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write.table(prediction, file = "${prefix}.csv", row.names = FALSE, quote = FALSE, dec = '.')
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version_file_path <- "versions.yml"
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version_file_path <- "versions.yml"
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version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
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version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
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@ -8,7 +8,7 @@ tools:
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- "ampir":
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- "ampir":
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description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale."
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description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale."
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homepage: "https://github.com/Legana/ampir"
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homepage: "https://github.com/Legana/ampir"
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documentation: "https://github.com/Legana/ampir"
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documentation: "https://cran.r-project.org/web/packages/ampir/index.html"
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tool_dev_url: "https://github.com/Legana/ampir"
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tool_dev_url: "https://github.com/Legana/ampir"
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doi: "10.1093/bioinformatics/btaa653"
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doi: "10.1093/bioinformatics/btaa653"
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licence: ["GPL v2"]
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licence: ["GPL v2"]
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@ -42,14 +42,14 @@ output:
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type: file
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type: file
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description: File containing software versions
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description: File containing software versions
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pattern: "versions.yml"
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pattern: "versions.yml"
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- amps:
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- amps_faa:
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type: file
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type: file
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description: File containing AMP predictions
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description: File containing AMP predictions in amino acid FASTA format
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pattern: "prediction.fasta"
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- output_name:
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type: value
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description: File name of the FASTA output file
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pattern: "*.{faa,fasta}"
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pattern: "*.{faa,fasta}"
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- amps_csv:
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type: file
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description: File containing AMP predictions in CSV format
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pattern: "*.csv"
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authors:
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authors:
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- "@jasmezz"
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- "@jasmezz"
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@ -14,7 +14,5 @@ workflow test_ampir {
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model = "precursor"
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model = "precursor"
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output_name = "prediction.fasta"
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AMPIR ( fasta, cut_off, model )
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AMPIR ( fasta, cut_off, model, output_name )
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}
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}
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@ -1,9 +1,11 @@
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- name: "ampir"
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- name: ampir test_ampir
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command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config -c ./tests/modules/ampir/nextflow.config
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command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config -c ./tests/modules/ampir/nextflow.config
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tags:
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tags:
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- "ampir"
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- ampir
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files:
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files:
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- path: output/ampir/prediction.fasta
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- path: output/ampir/test.csv
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md5sum: 063fd8866f6a669457d7a49404fb449f
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- path: output/ampir/test.faa
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md5sum: e605d38752fd90261c924d51f7007189
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md5sum: e605d38752fd90261c924d51f7007189
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- path: output/ampir/versions.yml
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- path: output/ampir/versions.yml
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md5sum: 4a11d25b8a904a7ffb34ae88f6826888
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md5sum: 4a11d25b8a904a7ffb34ae88f6826888
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