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Merge pull request #440 from genomic-medicine-sweden/add-retroseq-to-…
…pipeline Add mobile element calling to raredisease
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", | ||
| "title": "Schema for mobile_element_references", | ||
| "description": "Schema for the file provided with params.mobile_element_references", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "type": { | ||
| "type": "string", | ||
| "exists": true, | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "Mobile element type must be provided and cannot contain spaces" | ||
| }, | ||
| "path": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "exists": true, | ||
| "pattern": "^\\S+\\.bed$", | ||
| "errorMessage": "Bed file, cannot contain spaces and must have extension '.bed'" | ||
| } | ||
| }, | ||
| "required": ["type", "path"] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ext.when = Conditional clause | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
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| process { | ||
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| withName: '.*CALL_MOBILE_ELEMENTS:.*' { | ||
| publishDir = [ | ||
| enabled: false | ||
| ] | ||
| } | ||
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| withName: '.*CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT' { | ||
| ext.args = { [ | ||
| '--output-fmt bam', | ||
| '--fetch-pairs' | ||
| ].join(' ') } | ||
| ext.args2 = { "${meta.interval}" } | ||
| ext.prefix = { "${meta.id}_${meta.interval}" } | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER' { | ||
| ext.prefix = { "${meta.id}_${meta.interval}_retroseq_discover" } | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:RETROSEQ_CALL' { | ||
| ext.args = { '--soft' } | ||
| ext.prefix = { "${meta.id}_${meta.interval}_retroseq_call" } | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME' { | ||
| ext.args2 = { '--output-type v' } | ||
| ext.prefix = { "${meta.id}_${meta.interval}_retroseq_reheader" } | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME' { | ||
| ext.args = { '--output-type z' } | ||
| ext.prefix = { "${meta.id}_${meta.interval}_retroseq_sort" } | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME' { | ||
| ext.args = { '--output-type z --allow-overlaps' } | ||
| ext.prefix = { "${meta.id}_mobile_elements" } | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME' { | ||
| ext.args = { '--bnd_distance 150 --overlap 0.5' } | ||
| ext.prefix = { "${meta.id}_mobile_elements" } | ||
| publishDir = [ | ||
| path: { "${params.outdir}/call_mobile_elements" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: '.*CALL_MOBILE_ELEMENTS:TABIX_ME' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/call_mobile_elements" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| process RETROSEQ_CALL { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
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| conda "bioconda::perl-retroseq=1.5=pl5321hdfd78af_1" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' : 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' }" | ||
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| input: | ||
| tuple val(meta), path(tab), path(bam), path(bai) | ||
| tuple val(meta2), path(fasta) | ||
| tuple val(meta3), path(fai) | ||
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| output: | ||
| tuple val(meta), path("*.vcf"), emit: vcf | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = "1.5" | ||
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| """ | ||
| retroseq.pl \\ | ||
| -call \\ | ||
| $args \\ | ||
| -bam $bam \\ | ||
| -input $tab \\ | ||
| -ref $fasta \\ | ||
| -output ${prefix}.vcf | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| retroseq_call: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
|
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = "1.5" | ||
| """ | ||
| touch ${prefix}.vcf | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| retroseq_call: $VERSION | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: "retroseq_call" | ||
| description: RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) from next-gen sequencing reads aligned to a reference genome in BAM format. | ||
| keywords: | ||
| - retroseq | ||
| - transposable elements | ||
| - genomics | ||
| tools: | ||
| - "retroseq": | ||
| description: "RetroSeq: discovery and genotyping of TEVs from reads in BAM format." | ||
| homepage: "https://github.com/tk2/RetroSeq" | ||
| documentation: "https://github.com/tk2/RetroSeq" | ||
| tool_dev_url: "https://github.com/tk2/RetroSeq" | ||
| doi: "10.1093/bioinformatics/bts697" | ||
| licence: "['GPL']" | ||
|
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| input: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', single_end:false ]` | ||
| - tab: | ||
| type: file | ||
| description: Output file from running retroseq -call | ||
| pattern: "*.tab" | ||
| - bam: | ||
| type: file | ||
| description: Sorted BAM file | ||
| pattern: "*.bam" | ||
| - bai: | ||
| type: file | ||
| description: Index of the sorted BAM file | ||
| pattern: "*.bam" | ||
| - meta2: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', single_end:false ]` | ||
| - fasta: | ||
| type: file | ||
| description: Reference genome in fasta format | ||
| pattern: "*.fasta" | ||
| - meta3: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', single_end:false ]` | ||
| - fai: | ||
| type: file | ||
| description: Reference FASTA index | ||
| pattern: "*.fai" | ||
|
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| output: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', single_end:false ]` | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| - vcf: | ||
| type: file | ||
| description: Output file containing TEVs and their location in the genome. | ||
| pattern: "*.vcf" | ||
|
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| authors: | ||
| - "@peterpru" |
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