add severus

modules/nf-core/severus/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "severus"
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - "bioconda::severus=1.1"

modules/nf-core/severus/main.nf

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+process SEVERUS {
+ tag "$meta.id"
+ label 'process_medium'
+
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/severus:1.1--pyhdfd78af_0':
+ 'biocontainers/severus:1.1--pyhdfd78af_0' }"
+
+ input:
+ tuple val(meta), path(target_bam), path(target_index), path(control_bam), path(control_index), path(vcf)
+ tuple val(meta2), path(bed)
+
+ output:
+ tuple val(meta), path("${prefix}/severus.log") , emit: log
+ tuple val(meta), path("${prefix}/read_qual.txt") , emit: read_qual
+ tuple val(meta), path("${prefix}/breakpoints_double.csv") , emit: breakpoints_double
+ tuple val(meta), path("${prefix}/read_alignments") , emit: read_alignments , optional: true
+ tuple val(meta), path("${prefix}/read_ids.csv") , emit: read_ids , optional: true
+ tuple val(meta), path("${prefix}/severus_collaped_dup.bed") , emit: collapsed_dup , optional: true
+ tuple val(meta), path("${prefix}/severus_LOH.bed") , emit: loh , optional: true
+ tuple val(meta), path("${prefix}/all_SVs/severus_all.vcf") , emit: all_vcf , optional: true
+ tuple val(meta), path("${prefix}/all_SVs/breakpoints_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true
+ tuple val(meta), path("${prefix}/all_SVs/breakpoints_clusters.tsv") , emit: all_breakpoints_clusters , optional: true
+ tuple val(meta), path("${prefix}/all_SVs/plots/severus_*.html") , emit: all_plots , optional: true
+ tuple val(meta), path("${prefix}/somatic_SVs/severus_all.vcf") , emit: somatic_vcf , optional: true
+ tuple val(meta), path("${prefix}/somatic_SVs/breakpoints_clusters_list.tsv"), emit: somatic_breakpoints_clusters_list, optional: true
+ tuple val(meta), path("${prefix}/somatic_SVs/breakpoints_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true
+ tuple val(meta), path("${prefix}/somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ prefix = task.ext.prefix ?: "${meta.id}"
+
+ def control = control_bam ? "--control-bam ${control_bam}" : ""
+ def vntr_bed = bed ? "--vntr-bed ${bed}" : ""
+ def phasing_vcf = vcf ? "--phasing-vcf ${vcf}" : ""
+ """
+ severus \\
+ $args \\
+ --threads $task.cpus \\
+ --target-bam $target_bam \\
+ $vntr_bed \\
+ $control \\
+ $phasing_vcf \\
+ --out-dir ${prefix}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ severus: \$(severus --version)
+ END_VERSIONS
+ """
+
+ stub:
+ def args = task.ext.args ?: ''
+ prefix = task.ext.prefix ?: "${meta.id}"
+
+ """
+ mkdir -p ${prefix}/all_SVs/plots
+ mkdir -p ${prefix}/somatic_SVs/plots
+
+ touch ${prefix}/severus_collaped_dup.bed
+ touch ${prefix}/severus.log
+ touch ${prefix}/severus_LOH.bed
+ touch ${prefix}/read_alignments
+ touch ${prefix}/read_ids.csv
+ touch ${prefix}/read_qual.txt
+ touch ${prefix}/breakpoints_double.csv
+ touch ${prefix}/all_SVs/severus_all.vcf
+ touch ${prefix}/all_SVs/breakpoints_clusters_list.tsv
+ touch ${prefix}/all_SVs/breakpoints_clusters.tsv
+ touch ${prefix}/all_SVs/plots/severus_0.html
+ touch ${prefix}/all_SVs/plots/severus_1.html
+ touch ${prefix}/somatic_SVs/severus_somatic.vcf
+ touch ${prefix}/somatic_SVs/breakpoints_clusters_list.tsv
+ touch ${prefix}/somatic_SVs/breakpoints_clusters.tsv
+ touch ${prefix}/somatic_SVs/plots/severus_0.html
+ touch ${prefix}/somatic_SVs/plots/severus_1.html
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ severus: \$(severus --version)
+ END_VERSIONS
+ """
+}

modules/nf-core/severus/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "severus"
+description: Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
+keywords:
+ - structural
+ - variation
+ - somatic
+ - germline
+ - long-read
+tools:
+ - "severus":
+ description: "A tool for somatic structural variant calling using long reads"
+ homepage: "https://github.com/KolmogorovLab/Severus"
+ documentation: "https://github.com/KolmogorovLab/Severus"
+ tool_dev_url: "https://github.com/KolmogorovLab/Severus"
+ doi: "10.1101/2024.03.22.24304756"
+ licence: ["BSD-3-clause"]
+
+input:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - target_bam:
+ type: file
+ description: path to one or multiple target bam files (e.g. tumor, must be indexed)
+ pattern: "*.bam"
+ - target_index:
+ type: file
+ description: path to one or multiple target bam index files
+ pattern: "*.bai"
+ - control_bam:
+ type: file
+ description: path to the control bam file (e.g. normal, must be indexed)
+ pattern: "*.bam"
+ - control_index:
+ type: file
+ description: path to the control bam file index
+ pattern: "*.bai"
+ - vcf:
+ type: file
+ description: path to vcf file used for phasing (if using haplotype specific SV calling
+ pattern: "*.{vcf,vcf.gz}"
+ - meta2:
+ type: map
+ description: |
+ Groovy Map containing tandem repeat regions information
+ e.g. `[ id:'hg38']`
+ - bed:
+ type: file
+ description: path to bed file for tandem repeat regions (must be ordered)
+ pattern: "*.bed"
+output:
+ - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. `[ id:'sample1', single_end:false ]`
+ - versions:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+ - log:
+ type: file
+ description: Severus log file
+ pattern: "${prefix}/severus.log"
+ - read_qual:
+ type: file
+ description: Severus read_qual file
+ pattern: "${prefix}/read_qual.txt"
+ - breakpoints_double:
+ type: file
+ description: Severus breakpoints_double file
+ pattern: "${prefix}/breakpoints_double.csv"
+ - read_alignments:
+ type: file
+ description: read alignments file
+ pattern: "${prefix}/read_alignments"
+ - read_ids:
+ type: file
+ description: read IDs for support reads
+ pattern: "${prefix}/read_ids"
+ - collapsed_dup:
+ type: file
+ description: a bed file with identified collapsed duplication regions
+ pattern: "${prefix}/severus_collaped_dup"
+ - loh:
+ type: file
+ description: a bed file with identified collapsed duplication regions
+ pattern: "${prefix}/severus_LOH.bed"
+ - all_vcf:
+ type: file
+ description: VCF file with all SVs (somatic + germline)
+ pattern: "${prefix}/all_SVs/severus_all.vcf"
+ - all_breakpoints_clusters_list:
+ type: file
+ description: Severus breakpoints clusters list file
+ pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv"
+ - all_breakpoints_clusters:
+ type: file
+ description: Severus breakpoints clusters file
+ pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv"
+ - all_plots:
+ type: file
+ description: Severus plots
+ pattern: "${prefix}/all_SVs/plots/*.html"
+ - somatic_vcf:
+ type: file
+ description: VCF file with somatic SVs
+ pattern: "${prefix}/somatic_SVs/severus_all.vcf"
+ - somatic_breakpoints_clusters_list:
+ type: file
+ description: Severus somatic breakpoints clusters list file
+ pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv"
+ - somatic_breakpoints_clusters:
+ type: file
+ description: Severus somatic breakpoints clusters file
+ pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv"
+ - somatic_plots:
+ type: file
+ description: Severus somatic plots
+ pattern: "${prefix}/somatic_SVs/plots/*.html"
+authors:
+ - "@fellen31"
+maintainers:
+ - "@fellen31"