diff --git a/.github/filters.yml b/.github/filters.yml index 2bad1fb9..49916804 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -229,6 +229,10 @@ seacr_callpeak: - software/seacr/callpeak/** - tests/software/seacr/callpeak/** +seqwish_induce: + - software/seqwish/induce/** + - tests/software/seqwish/induce/** + star_align: - software/star/align/** - tests/software/star/align/** diff --git a/software/seqwish/induce/functions.nf b/software/seqwish/induce/functions.nf new file mode 100644 index 00000000..d25eea86 --- /dev/null +++ b/software/seqwish/induce/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)}/$args.filename" + } + } +} diff --git a/software/seqwish/induce/main.nf b/software/seqwish/induce/main.nf new file mode 100644 index 00000000..592058ab --- /dev/null +++ b/software/seqwish/induce/main.nf @@ -0,0 +1,44 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' +params.options = [:] +def options = initOptions(params.options) + +def VERSION = '0.4.1' + +process SEQWISH_INDUCE { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::seqwish=0.4.1" : null) + + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/seqwish:0.4.1--h8b12597_0" + } else { + container "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0" + } + + input: + tuple val(meta), path(paf), path(fasta) + + output: + tuple val(meta), path("*.gfa"), emit: gfa + path "*.version.txt" , emit: version + + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + seqwish \\ + --threads $task.cpus \\ + --paf-alns=$paf \\ + --seqs=$fasta \\ + --gfa=${prefix}.gfa \\ + $options.args + + echo $VERSION > ${software}.version.txt + """ +} diff --git a/software/seqwish/induce/meta.yml b/software/seqwish/induce/meta.yml new file mode 100644 index 00000000..47bb5ac6 --- /dev/null +++ b/software/seqwish/induce/meta.yml @@ -0,0 +1,67 @@ +name: seqwish_induce +description: Induce a variation graph in GFA format from alignments in PAF format +keywords: + - induce + - paf + - gfa + - graph + - variation graph +tools: + - seqwish: + description: | + seqwish implements a lossless conversion from pairwise alignments between + sequences to a variation graph encoding the sequences and their alignments. + homepage: https://github.com/ekg/seqwish + documentation: https://github.com/ekg/seqwish +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$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 ] + - paf: + type: file + description: PAF file of alignments + pattern: "*.{paf,paf.gz}" + - fasta: + type: file + description: FASTA file used to generate alignments + pattern: "*.{fa,fa.gz,fasta,fasta.gz}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA1 format + pattern: "*.{gfa}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@heuermh" diff --git a/tests/data/paf/GCA_011545545.1_ASM1154554v1_cds_from_genomic.paf b/tests/data/paf/GCA_011545545.1_ASM1154554v1_cds_from_genomic.paf new file mode 100644 index 00000000..ead0b0d9 --- /dev/null +++ b/tests/data/paf/GCA_011545545.1_ASM1154554v1_cds_from_genomic.paf @@ -0,0 +1,11 @@ +lcl|MT192765.1_cds_QIK50426.1_1 21291 1 21289 + lcl|MT192765.1_cds_QIK50426.1_1 21291 1 21289 21288 21288 60 tp:A:P cm:i:3984 s1:i:21288 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50427.1_2 3822 8 3821 + lcl|MT192765.1_cds_QIK50427.1_2 3822 8 3821 3813 3813 60 tp:A:P cm:i:722 s1:i:3813 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50428.1_3 828 4 819 + lcl|MT192765.1_cds_QIK50428.1_3 828 4 819 815 815 60 tp:A:P cm:i:148 s1:i:815 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50429.1_4 228 6 226 + lcl|MT192765.1_cds_QIK50429.1_4 228 6 226 220 220 60 tp:A:P cm:i:42 s1:i:220 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50430.1_5 669 6 663 + lcl|MT192765.1_cds_QIK50430.1_5 669 6 663 657 657 60 tp:A:P cm:i:115 s1:i:657 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50431.1_6 186 0 185 + lcl|MT192765.1_cds_QIK50431.1_6 186 0 185 185 185 60 tp:A:P cm:i:33 s1:i:185 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50432.1_7 366 1 358 + lcl|MT192765.1_cds_QIK50432.1_7 366 1 358 357 357 60 tp:A:P cm:i:64 s1:i:357 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50433.1_8 132 6 124 + lcl|MT192765.1_cds_QIK50433.1_8 132 6 124 118 118 60 tp:A:P cm:i:20 s1:i:118 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50434.1_9 366 6 357 + lcl|MT192765.1_cds_QIK50434.1_9 366 6 357 351 351 60 tp:A:P cm:i:68 s1:i:351 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50435.1_10 1260 4 1255 + lcl|MT192765.1_cds_QIK50435.1_10 1260 4 1255 1251 1251 60 tp:A:P cm:i:231 s1:i:1251 s2:i:0 dv:f:0 rl:i:0 +lcl|MT192765.1_cds_QIK50436.1_11 117 0 116 + lcl|MT192765.1_cds_QIK50436.1_11 117 0 116 116 116 60 tp:A:P cm:i:19 s1:i:116 s2:i:0 dv:f:0 rl:i:0 diff --git a/tests/software/seqwish/induce/main.nf b/tests/software/seqwish/induce/main.nf new file mode 100644 index 00000000..1d690eb8 --- /dev/null +++ b/tests/software/seqwish/induce/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SEQWISH_INDUCE } from '../../../../software/seqwish/induce/main.nf' addParams( options: [:] ) + +workflow test_seqwish_induce { + + def input = [] + input = [ [ id:'GCA_011545545.1_ASM1154554v1_cds_from_genomic' ], // meta map + [ file("${launchDir}/tests/data/paf/GCA_011545545.1_ASM1154554v1_cds_from_genomic.paf", checkIfExists: true) ], + [ file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true) ] ] + + SEQWISH_INDUCE ( input ) +} \ No newline at end of file diff --git a/tests/software/seqwish/induce/test.yml b/tests/software/seqwish/induce/test.yml new file mode 100644 index 00000000..3da08b27 --- /dev/null +++ b/tests/software/seqwish/induce/test.yml @@ -0,0 +1,8 @@ +- name: seqwish induce + command: nextflow run ./tests/software/seqwish/induce -entry test_seqwish_induce -c tests/config/nextflow.config + tags: + - seqwish + - seqwish_induce + files: + - path: output/seqwish/GCA_011545545.1_ASM1154554v1_cds_from_genomic.gfa + md5sum: 216a02d3aca322a457c31a62c628548e \ No newline at end of file