From c2aa95cb6cc47999a1823cd2c417fec5f879eaf4 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 23 Mar 2021 05:51:23 -0400 Subject: [PATCH] add prokka module (#298) * add prokka module * adjust test outputs * fix prokka command * adjust test outputs * handle optional input * update pytest * update pytest * adjust test outputs * adjust test outputs * switch to lists for optional inputs, add md5sums for non-timestamped outputs * add optional prodigal training file * add optional prodigal training info to meta yaml --- software/prokka/functions.nf | 60 +++++++++++++++++++++ software/prokka/main.nf | 56 ++++++++++++++++++++ software/prokka/meta.yml | 91 ++++++++++++++++++++++++++++++++ tests/config/pytest_software.yml | 4 ++ tests/software/prokka/main.nf | 12 +++++ tests/software/prokka/test.yml | 27 ++++++++++ 6 files changed, 250 insertions(+) create mode 100644 software/prokka/functions.nf create mode 100644 software/prokka/main.nf create mode 100644 software/prokka/meta.yml create mode 100644 tests/software/prokka/main.nf create mode 100644 tests/software/prokka/test.yml diff --git a/software/prokka/functions.nf b/software/prokka/functions.nf new file mode 100644 index 00000000..f177f0c8 --- /dev/null +++ b/software/prokka/functions.nf @@ -0,0 +1,60 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/prokka/main.nf b/software/prokka/main.nf new file mode 100644 index 00000000..66b5a665 --- /dev/null +++ b/software/prokka/main.nf @@ -0,0 +1,56 @@ +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process PROKKA { + tag "$meta.id" + label 'prokka' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl526_0" + } else { + container "quay.io/biocontainers/prokka:1.14.6--pl526_0" + } + + input: + tuple val(meta), path(fasta) + path proteins + path prodigal_tf + + output: + tuple val(meta), path("${prefix}/*.gff"), emit: gff + tuple val(meta), path("${prefix}/*.gbk"), emit: gbk + tuple val(meta), path("${prefix}/*.fna"), emit: fna + tuple val(meta), path("${prefix}/*.faa"), emit: faa + tuple val(meta), path("${prefix}/*.ffn"), emit: ffn + tuple val(meta), path("${prefix}/*.sqn"), emit: sqn + tuple val(meta), path("${prefix}/*.fsa"), emit: fsa + tuple val(meta), path("${prefix}/*.tbl"), emit: tbl + tuple val(meta), path("${prefix}/*.err"), emit: err + tuple val(meta), path("${prefix}/*.log"), emit: log + tuple val(meta), path("${prefix}/*.txt"), emit: txt + tuple val(meta), path("${prefix}/*.tsv"), emit: tsv + path "*.version.txt", emit: version + + script: + def software = getSoftwareName(task.process) + prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def proteins_opt = proteins ? "--proteins ${proteins[0]}" : "" + def prodigal_opt = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : "" + """ + prokka \\ + $options.args \\ + --cpus $task.cpus \\ + --prefix $prefix \\ + $proteins_opt \\ + $prodigal_tf \\ + $fasta + + echo \$(prokka --version 2>&1) | sed 's/^.*prokka //' > ${software}.version.txt + """ +} diff --git a/software/prokka/meta.yml b/software/prokka/meta.yml new file mode 100644 index 00000000..4489b2fd --- /dev/null +++ b/software/prokka/meta.yml @@ -0,0 +1,91 @@ +name: prokka +description: Whole genome annotation of small genomes (bacterial, archeal, viral) +keywords: + - annotation + - fasta + - prokka +tools: + - prokka: + description: Rapid annotation of prokaryotic genomes + homepage: https://github.com/tseemann/prokka + doi: "10.1093/bioinformatics/btu153" + licence: ['GPL v2'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + FASTA file to be annotated. Has to contain at least a non-empty string dummy value. + - proteins: + type: file + description: FASTA file of trusted proteins to first annotate from (optional) + - prodigal_tf: + type: file + description: Training file to use for Prodigal (optional) + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + - gff: + type: file + description: annotation in GFF3 format, containing both sequences and annotations + pattern: "*.{gff}" + - gbk: + type: file + description: annotation in GenBank format, containing both sequences and annotations + pattern: "*.{gbk}" + - fna: + type: file + description: nucleotide FASTA file of the input contig sequences + pattern: "*.{fna}" + - faa: + type: file + description: protein FASTA file of the translated CDS sequences + pattern: "*.{faa}" + - ffn: + type: file + description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) + pattern: "*.{ffn}" + - sqn: + type: file + description: an ASN1 format "Sequin" file for submission to Genbank + pattern: "*.{sqn}" + - fsa: + type: file + description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file + pattern: "*.{fsa}" + - tbl: + type: file + description: feature Table file, used by "tbl2asn" to create the .sqn file + pattern: "*.{tbl}" + - err: + type: file + description: unacceptable annotations - the NCBI discrepancy report. + pattern: "*.{err}" + - log: + type: file + description: contains all the output that Prokka produced during its run + pattern: "*.{log}" + - txt: + type: file + description: statistics relating to the annotated features found + pattern: "*.{txt}" + - tsv: + type: file + description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product) + pattern: "*.{tsv}" + +authors: + - "@rpetit3" diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index 2d459f88..3cccc596 100755 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -283,6 +283,10 @@ preseq_lcextrap: - software/preseq/lcextrap/** - tests/software/preseq/lcextrap/** +prokka: + - software/prokka/** + - tests/software/prokka/** + qualimap_bamqc: - software/qualimap/bamqc/** - tests/software/qualimap/bamqc/** diff --git a/tests/software/prokka/main.nf b/tests/software/prokka/main.nf new file mode 100644 index 00000000..60df886b --- /dev/null +++ b/tests/software/prokka/main.nf @@ -0,0 +1,12 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PROKKA } from '../../../software/prokka/main.nf' addParams( options: [:] ) + +workflow test_prokka { + def input = [] + input = [ [ id:'test', single_end:false ], // meta map + file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true), ] + PROKKA ( input, [], [] ) +} diff --git a/tests/software/prokka/test.yml b/tests/software/prokka/test.yml new file mode 100644 index 00000000..fc12af81 --- /dev/null +++ b/tests/software/prokka/test.yml @@ -0,0 +1,27 @@ +- name: prokka + command: nextflow run ./tests/software/prokka -entry test_prokka -c tests/config/nextflow.config + tags: + - prokka + files: + - path: output/prokka/test/test.err + md5sum: b3daedc646fddd422824e2b3e5e9229d + - path: output/prokka/test/test.faa + md5sum: a4ceda83262b3c222a6b1f508fb9e24b + - path: output/prokka/test/test.ffn + md5sum: 80f474b5367b7ea5ed23791935f65e34 + - path: output/prokka/test/test.fna + md5sum: 787307f29a263e5657cc276ebbf7e2b3 + - path: output/prokka/test/test.fsa + md5sum: 71bbefcb7f12046bcd3263f58cfd5404 + - path: output/prokka/test/test.gff + md5sum: 5dbfb8fcf2db020564c16045976a0933 + - path: output/prokka/test/test.tbl + md5sum: d8f816a066ced94b62d9618b13fb8add + - path: output/prokka/test/test.tsv + md5sum: da7c720c3018c5081d6a70b517b7d450 + - path: output/prokka/test/test.txt + md5sum: b40e485ffc8eaf1feacf8d79d9751a33 + # Contain time stamps + - path: output/prokka/test/test.gbk + - path: output/prokka/test/test.log + - path: output/prokka/test/test.sqn