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Merge pull request #240 from AntoniaSchuster/dev
Add Prodigal
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| // | ||
| // Utility functions used in nf-core DSL2 module files | ||
| // | ||
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| // | ||
| // Extract name of software tool from process name using $task.process | ||
| // | ||
| def getSoftwareName(task_process) { | ||
| return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() | ||
| } | ||
|
|
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| // | ||
| // Extract name of module from process name using $task.process | ||
| // | ||
| def getProcessName(task_process) { | ||
| return task_process.tokenize(':')[-1] | ||
| } | ||
|
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| // | ||
| // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules | ||
| // | ||
| def initOptions(Map args) { | ||
| def Map options = [:] | ||
| options.args = args.args ?: '' | ||
| options.args2 = args.args2 ?: '' | ||
| options.args3 = args.args3 ?: '' | ||
| options.publish_by_meta = args.publish_by_meta ?: [] | ||
| options.publish_dir = args.publish_dir ?: '' | ||
| options.publish_files = args.publish_files | ||
| options.suffix = args.suffix ?: '' | ||
| return options | ||
| } | ||
|
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| // | ||
| // Tidy up and join elements of a list to return a path string | ||
| // | ||
| def getPathFromList(path_list) { | ||
| def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries | ||
| paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes | ||
| return paths.join('/') | ||
| } | ||
|
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| // | ||
| // Function to save/publish module results | ||
| // | ||
| def saveFiles(Map args) { | ||
| def ioptions = initOptions(args.options) | ||
| def path_list = [ ioptions.publish_dir ?: args.publish_dir ] | ||
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| // Do not publish versions.yml unless running from pytest workflow | ||
| if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { | ||
| return null | ||
| } | ||
| if (ioptions.publish_by_meta) { | ||
| def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta | ||
| for (key in key_list) { | ||
| if (args.meta && key instanceof String) { | ||
| def path = key | ||
| if (args.meta.containsKey(key)) { | ||
| path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] | ||
| } | ||
| path = path instanceof String ? path : '' | ||
| path_list.add(path) | ||
| } | ||
| } | ||
| } | ||
| if (ioptions.publish_files instanceof Map) { | ||
| for (ext in ioptions.publish_files) { | ||
| if (args.filename.endsWith(ext.key)) { | ||
| def ext_list = path_list.collect() | ||
| ext_list.add(ext.value) | ||
| return "${getPathFromList(ext_list)}/$args.filename" | ||
| } | ||
| } | ||
| } else if (ioptions.publish_files == null) { | ||
| return "${getPathFromList(path_list)}/$args.filename" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| // Import generic module functions | ||
| include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' | ||
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| params.options = [:] | ||
| options = initOptions(params.options) | ||
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| process PRODIGAL { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
| publishDir "${params.outdir}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } | ||
|
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| conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null) | ||
| if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { | ||
| container "https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2" | ||
| } else { | ||
| container "quay.io/biocontainers/prodigal:2.6.3--h516909a_2" | ||
| } | ||
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| input: | ||
| tuple val(meta), path(genome) | ||
| val(output_format) | ||
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| output: | ||
| tuple val(meta), path("${prefix}.${output_format}"), emit: gene_annotations | ||
| tuple val(meta), path("${prefix}.fna"), emit: nucleotide_fasta | ||
| tuple val(meta), path("${prefix}.faa"), emit: amino_acid_fasta | ||
| tuple val(meta), path("${prefix}_all.txt"), emit: all_gene_annotations | ||
| path "versions.yml" , emit: versions | ||
|
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| script: | ||
| prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" | ||
| """ | ||
| prodigal -i "${genome}" \\ | ||
| $options.args \\ | ||
| -f $output_format \\ | ||
| -d "${prefix}.fna" \\ | ||
| -o "${prefix}.${output_format}" \\ | ||
| -a "${prefix}.faa" \\ | ||
| -s "${prefix}_all.txt" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| ${getProcessName(task.process)}: | ||
| ${getSoftwareName(task.process)}: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| name: prodigal | ||
| description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program | ||
| keywords: | ||
| - sort | ||
| tools: | ||
| - prodigal: | ||
| description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program | ||
| homepage: {} | ||
| documentation: {} | ||
| tool_dev_url: {} | ||
| doi: "" | ||
| licence: ["GPL v3"] | ||
|
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||
| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - bam: | ||
| type: file | ||
| description: BAM/CRAM/SAM file | ||
| pattern: "*.{bam,cram,sam}" | ||
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| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - bam: | ||
| type: file | ||
| description: Sorted BAM/CRAM/SAM file | ||
| pattern: "*.{bam,cram,sam}" | ||
|
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||
| authors: | ||
| - "@grst" |
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