diff --git a/.github/filters.yml b/.github/filters.yml index dee0b0b2..a55df261 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -148,6 +148,10 @@ ivar_trim: - software/ivar/trim/** - tests/software/ivar/trim/** +ivar_variants: + - software/ivar/variants/** + - tests/software/ivar/variants/** + minimap2_align: - software/minimap2/align/** - tests/software/minimap2/align/** diff --git a/software/ivar/variants/functions.nf b/software/ivar/variants/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/ivar/variants/functions.nf @@ -0,0 +1,59 @@ +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf new file mode 100644 index 00000000..1f940d67 --- /dev/null +++ b/software/ivar/variants/main.nf @@ -0,0 +1,50 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process IVAR_VARIANTS { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0" + } else { + container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0" + } + + input: + tuple val(meta), path(bam) + path fasta + path gff + + output: + tuple val(meta), path("*.tsv") , emit: tsv + tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" + def features = params.gff ? "-g $gff" : "" + """ + samtools mpileup \\ + $options.args2 \\ + --reference $fasta \\ + $bam | \\ + $save_mpileup \\ + ivar variants \\ + $options.args \\ + $features \\ + -r $fasta \\ + -p $prefix + + ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt + """ +} diff --git a/software/ivar/variants/meta.yml b/software/ivar/variants/meta.yml new file mode 100644 index 00000000..6f8e828a --- /dev/null +++ b/software/ivar/variants/meta.yml @@ -0,0 +1,72 @@ +name: ivar_variants +description: Call variants from a BAM file using iVar +keywords: + - amplicon sequencing + - variants + - fasta +tools: + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file + pattern: "*.bam" + - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM file + pattern: "*.fa" + - gff: + type: file + description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. + patter: "*.gff" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tsv: + type: file + description: iVar generated TSV file with the variants + pattern: "*.tsv" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@andersgs" + - "@drpatelh" diff --git a/tests/data/gff/sarscov2/MN908947.3.gff3 b/tests/data/gff/sarscov2/MN908947.3.gff3 new file mode 100644 index 00000000..d5cf08a5 --- /dev/null +++ b/tests/data/gff/sarscov2/MN908947.3.gff3 @@ -0,0 +1,27 @@ +##sequence-region MN908947.3 1 29903 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049 +MN908947.3 Genbank region 1 29903 . + . ID=MN908947.3:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gb-acronym=SARS-CoV-2;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus +MN908947.3 Genbank five_prime_UTR 1 265 . + . ID=id-MN908947.3:1..265;gbkey=5'UTR +MN908947.3 Genbank gene 266 21555 . + . ID=gene-orf1ab;Name=orf1ab;gbkey=Gene;gene=orf1ab;gene_biotype=protein_coding +MN908947.3 Genbank CDS 266 13468 . + 0 ID=cds-QHD43415.1;Parent=gene-orf1ab;Dbxref=NCBI_GP:QHD43415.1;Name=QHD43415.1;Note=translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=orf1ab;part=1;product=orf1ab polyprotein;protein_id=QHD43415.1 +MN908947.3 Genbank CDS 13468 21555 . + 0 ID=cds-QHD43415.1;Parent=gene-orf1ab;Dbxref=NCBI_GP:QHD43415.1;Name=QHD43415.1;Note=translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=orf1ab;part=2;product=orf1ab polyprotein;protein_id=QHD43415.1 +MN908947.3 Genbank gene 21563 25384 . + . ID=gene-S;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding +MN908947.3 Genbank CDS 21563 25384 . + 0 ID=cds-QHD43416.1;Parent=gene-S;Dbxref=NCBI_GP:QHD43416.1;Name=QHD43416.1;Note=structural protein;gbkey=CDS;gene=S;product=surface glycoprotein;protein_id=QHD43416.1 +MN908947.3 Genbank gene 25393 26220 . + . ID=gene-ORF3a;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding +MN908947.3 Genbank CDS 25393 26220 . + 0 ID=cds-QHD43417.1;Parent=gene-ORF3a;Dbxref=NCBI_GP:QHD43417.1;Name=QHD43417.1;gbkey=CDS;gene=ORF3a;product=ORF3a protein;protein_id=QHD43417.1 +MN908947.3 Genbank gene 26245 26472 . + . ID=gene-E;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding +MN908947.3 Genbank CDS 26245 26472 . + 0 ID=cds-QHD43418.1;Parent=gene-E;Dbxref=NCBI_GP:QHD43418.1;Name=QHD43418.1;Note=structural protein%3B E protein;gbkey=CDS;gene=E;product=envelope protein;protein_id=QHD43418.1 +MN908947.3 Genbank gene 26523 27191 . + . ID=gene-M;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding +MN908947.3 Genbank CDS 26523 27191 . + 0 ID=cds-QHD43419.1;Parent=gene-M;Dbxref=NCBI_GP:QHD43419.1;Name=QHD43419.1;Note=structural protein;gbkey=CDS;gene=M;product=membrane glycoprotein;protein_id=QHD43419.1 +MN908947.3 Genbank gene 27202 27387 . + . ID=gene-ORF6;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding +MN908947.3 Genbank CDS 27202 27387 . + 0 ID=cds-QHD43420.1;Parent=gene-ORF6;Dbxref=NCBI_GP:QHD43420.1;Name=QHD43420.1;gbkey=CDS;gene=ORF6;product=ORF6 protein;protein_id=QHD43420.1 +MN908947.3 Genbank gene 27394 27759 . + . ID=gene-ORF7a;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding +MN908947.3 Genbank CDS 27394 27759 . + 0 ID=cds-QHD43421.1;Parent=gene-ORF7a;Dbxref=NCBI_GP:QHD43421.1;Name=QHD43421.1;gbkey=CDS;gene=ORF7a;product=ORF7a protein;protein_id=QHD43421.1 +MN908947.3 Genbank gene 27894 28259 . + . ID=gene-ORF8;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding +MN908947.3 Genbank CDS 27894 28259 . + 0 ID=cds-QHD43422.1;Parent=gene-ORF8;Dbxref=NCBI_GP:QHD43422.1;Name=QHD43422.1;gbkey=CDS;gene=ORF8;product=ORF8 protein;protein_id=QHD43422.1 +MN908947.3 Genbank gene 28274 29533 . + . ID=gene-N;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding +MN908947.3 Genbank CDS 28274 29533 . + 0 ID=cds-QHD43423.2;Parent=gene-N;Dbxref=NCBI_GP:QHD43423.2;Name=QHD43423.2;Note=structural protein;gbkey=CDS;gene=N;product=nucleocapsid phosphoprotein;protein_id=QHD43423.2 +MN908947.3 Genbank gene 29558 29674 . + . ID=gene-ORF10;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding +MN908947.3 Genbank CDS 29558 29674 . + 0 ID=cds-QHI42199.1;Parent=gene-ORF10;Dbxref=NCBI_GP:QHI42199.1;Name=QHI42199.1;gbkey=CDS;gene=ORF10;product=ORF10 protein;protein_id=QHI42199.1 +MN908947.3 Genbank three_prime_UTR 29675 29903 . + . ID=id-MN908947.3:29675..29903;gbkey=3'UTR + diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf new file mode 100644 index 00000000..306d4585 --- /dev/null +++ b/tests/software/ivar/variants/main.nf @@ -0,0 +1,41 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:]) + +workflow test_ivar_variants_no_gff_no_mpileup { + params.gff = false + params.save_mpileup = false + + def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) + def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true) + def input = [] + input = [ [ id:'test'], + file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ] + IVAR_VARIANTS ( input, ref, dummy ) +} + +workflow test_ivar_variants_no_gff_with_mpileup { + params.gff = false + params.save_mpileup = true + + def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) + def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true) + def input = [] + input = [ [ id:'test'], + file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ] + IVAR_VARIANTS ( input, ref, dummy ) +} + +workflow test_ivar_variants_with_gff_with_mpileup { + params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3" + params.save_mpileup = true + + def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) + def gff = file(params.gff, checkIfExists: true) + def input = [] + input = [ [ id:'test'], + file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ] + IVAR_VARIANTS ( input, ref, gff ) +} diff --git a/tests/software/ivar/variants/test.yml b/tests/software/ivar/variants/test.yml new file mode 100644 index 00000000..ac78d3d1 --- /dev/null +++ b/tests/software/ivar/variants/test.yml @@ -0,0 +1,30 @@ +- name: ivar variants no gff no mpileup + command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c tests/config/nextflow.config + tags: + - ivar + - ivar_variants + files: + - path: output/ivar/test.tsv + md5sum: 3fd376b8ad80f27a999edf3345d2014a + +- name: ivar variants no gff with mpileup + command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config --save_mpileup + tags: + - ivar + - ivar_variants + files: + - path: output/ivar/test.tsv + md5sum: 3fd376b8ad80f27a999edf3345d2014a + - path: output/ivar/test.mpileup + md5sum: b3dfd337dfcd313d6cc9680d7e796fe6 + +- name: ivar variants with gff with mpileup + command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup + tags: + - ivar + - ivar_variants + files: + - path: output/ivar/test.tsv + md5sum: 3fd376b8ad80f27a999edf3345d2014a + - path: output/ivar/test.mpileup + md5sum: b3dfd337dfcd313d6cc9680d7e796fe6 \ No newline at end of file