diff --git a/software/spades/functions.nf b/software/spades/functions.nf new file mode 100644 index 00000000..f177f0c8 --- /dev/null +++ b/software/spades/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)}/$args.filename" + } + } +} diff --git a/software/spades/main.nf b/software/spades/main.nf new file mode 100644 index 00000000..badceb76 --- /dev/null +++ b/software/spades/main.nf @@ -0,0 +1,69 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process SPADES { + tag "$meta.id" + label 'process_high' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::spades=3.15.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0" + } else { + container "quay.io/biocontainers/spades:3.15.0--h633aebb_0" + } + + input: + tuple val(meta), path(reads) + path hmm + val coronaspades + + output: + tuple val(meta), path('*.scaffolds.fa') , optional:true, emit: scaffolds + tuple val(meta), path('*.contigs.fa') , optional:true, emit: contigs + tuple val(meta), path('*.transcripts.fa') , optional:true, emit: transcripts + tuple val(meta), path('*.gene_clusters.fa'), optional:true, emit: gene_clusters + tuple val(meta), path('*.assembly.gfa') , optional:true, emit: gfa + tuple val(meta), path('*.log') , emit: log + path '*.version.txt' , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}" + def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : "" + def command = coronaspades ? "coronaspades.py" : "spades.py" + """ + $command \\ + $options.args \\ + --threads $task.cpus \\ + $custom_hmms \\ + $input_reads \\ + -o ./ + mv spades.log ${prefix}.spades.log + + if [ -f scaffolds.fasta ]; then + mv scaffolds.fasta ${prefix}.scaffolds.fa + fi + if [ -f contigs.fasta ]; then + mv contigs.fasta ${prefix}.contigs.fa + fi + if [ -f transcripts.fasta ]; then + mv transcripts.fasta ${prefix}.transcripts.fa + fi + if [ -f assembly_graph_with_scaffolds.gfa ]; then + mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa + fi + + if [ -f gene_clusters.fasta ]; then + mv gene_clusters.fasta ${prefix}.gene_clusters.fa + fi + + echo \$(spades.py --version 2>&1) | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/spades/meta.yml b/software/spades/meta.yml new file mode 100644 index 00000000..d1ea7de3 --- /dev/null +++ b/software/spades/meta.yml @@ -0,0 +1,74 @@ +name: spades +description: Assembles a small genome (bacterial, fungal, viral) +keywords: + - genome + - assembly + - genome assembler + - small genome + - de novo assembler +tools: + - spades: + description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. + homepage: http://cab.spbu.ru/files/release3.15.0/manual.html + documentation: http://cab.spbu.ru/files/release3.15.0/manual.html + tool_dev_url: https://github.com/ablab/spades + doi: 10.1089/cmb.2012.0021 + licence: ['GPL v2'] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - hmm: + type: file + description: + File or directory with amino acid HMMs for Spades HMM-guided mode. + - coronaspades: + type: boolean + description: | + Run coronaspades instead of default spades mode. coronaSPAdes is a special + mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffolds: + type: file + description: | + Fasta file containing scaffolds + - contigs: + type: file + description: | + Fasta file containing contigs + - transcripts: + type: file + description: | + Fasta file containing transcripts + - gene_clusters: + type: file + description: | + Fasta file containing gene_clusters + - gfa: + type: file + description: | + gfa file containing assembly + - log: + type: file + description: | + Spades log file + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" + +authors: + - "@JoseEspinosa" + - "@drpatelh" diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index cd9c8395..11fbbd98 100644 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -144,6 +144,10 @@ gatk4_createsequencedictionary: - software/gatk4/createsequencedictionary/** - tests/software/gatk4/createsequencedictionary/** +gatk4_mergebamalignment: + - software/gatk4/mergebamalignment/** + - tests/software/gatk4/mergebamalignment/** + gatk4_mergevcfs: - software/gatk4/mergevcfs/** - tests/software/gatk4/mergevcfs/** @@ -160,6 +164,10 @@ gatk4_splitncigarreads: - software/gatk4/splitncigarreads/** - tests/software/gatk4/splitncigarreads/** +gatk4_variantfiltration: + - software/gatk4/variantfiltration/** + - tests/software/gatk4/variantfiltration/** + gffread: - software/gffread/** - tests/software/gffread/** @@ -289,6 +297,10 @@ seqwish_induce: - software/seqwish/induce/** - tests/software/seqwish/induce/** +spades: + - software/spades/** + - tests/software/spades/** + star_align: - software/star/align/** - tests/software/star/align/** @@ -325,10 +337,3 @@ untar: - software/untar/** - tests/software/untar/** -gatk4_mergebamalignment: - - software/gatk4/mergebamalignment/** - - tests/software/gatk4/mergebamalignment/** - -gatk4_variantfiltration: - - software/gatk4/variantfiltration/** - - tests/software/gatk4/variantfiltration/** diff --git a/tests/software/spades/main.nf b/tests/software/spades/main.nf new file mode 100644 index 00000000..4c473153 --- /dev/null +++ b/tests/software/spades/main.nf @@ -0,0 +1,52 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] ) + +workflow test_spades_single_end { + + def input = [] + def hmm = [] + def coronaspades = false + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] ] + + SPADES ( input, hmm, coronaspades ) +} + +workflow test_spades_paired_end { + + def input = [] + def hmm = [] + def coronaspades = false + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] ] + + SPADES ( input, hmm, coronaspades ) +} + +workflow test_coronospades_single_end { + + def input = [] + input = [ [ id:'test', single_end:true ], // meta map + [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ] + def hmm = [] + def coronaspades = true + + SPADES ( input, hmm, coronaspades ) +} + +workflow test_coronospades_paired_end { + + def input = [] + def hmm = [] + def coronaspades = true + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ] + + SPADES ( input, hmm, coronaspades ) +} + diff --git a/tests/software/spades/test.yml b/tests/software/spades/test.yml new file mode 100644 index 00000000..a54f83dd --- /dev/null +++ b/tests/software/spades/test.yml @@ -0,0 +1,58 @@ +- name: spades single end + command: nextflow run ./tests/software/spades -entry test_spades_single_end -c tests/config/nextflow.config + tags: + - spades + - spades_single_end + files: + - path: output/spades/test.assembly.gfa + md5sum: f15ad4a198324de37c6010dafb3fe781 + - path: output/spades/test.contigs.fa + md5sum: bc21771042b465c26dfc85beedc33d58 + - path: output/spades/test.scaffolds.fa + md5sum: bc21771042b465c26dfc85beedc33d58 + - path: output/spades/test.spades.log + - path: output/spades/warnings.log + +- name: spades paired end + command: nextflow run ./tests/software/spades -entry test_spades_paired_end -c tests/config/nextflow.config + tags: + - spades + - spades_paired_end + files: + - path: output/spades/test.assembly.gfa + md5sum: 5da5b04c6fce549c77a209034a9c1e72 + - path: output/spades/test.contigs.fa + md5sum: 403b612d52edf390f662ab601873f09f + - path: output/spades/test.scaffolds.fa + md5sum: 49a9cbb29cee4d088e05e62eb4bc77c4 + - path: output/spades/test.spades.log + - path: output/spades/warnings.log + +- name: coronaspades single end + command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config + tags: + - spades + - coronaspades_single_end + files: + - path: output/spades/test.assembly.gfa + md5sum: 46531ec9b845c1a1cb469627688fecb7 + - path: output/spades/test.contigs.fa + md5sum: f2c4a48ebba560aa5c8fde04dbe905fc + - path: output/spades/test.scaffolds.fa + md5sum: f2c4a48ebba560aa5c8fde04dbe905fc + - path: output/spades/test.spades.log + +- name: coronaspades paired end + command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config + tags: + - spades + - coronaspades_paired_end + files: + - path: output/spades/test.assembly.gfa + md5sum: 46531ec9b845c1a1cb469627688fecb7 + - path: output/spades/test.contigs.fa + md5sum: f2c4a48ebba560aa5c8fde04dbe905fc + - path: output/spades/test.scaffolds.fa + md5sum: f2c4a48ebba560aa5c8fde04dbe905fc + - path: output/spades/test.spades.log +