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Optional output from the VEP-moduel (#1775)
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774 * Trying to fix tests * Still trying to fix tests * Fetching the vep-output-file-extension from the args. * Update meta.yml * WIP: Adding tests for vep-output json and tab * updated the test.yml Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
This commit is contained in:
Anders Sune Pedersen
GitHub
parent
9dbaffff88
commit
30f72e2482
5 changed files with 97 additions and 13 deletions
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@ -17,25 +17,26 @@ process ENSEMBLVEP {
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path extra_files
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output:
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tuple val(meta), path("*.ann.vcf"), emit: vcf
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path "*.summary.html" , emit: report
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.ann.vcf") , optional:true, emit: vcf
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tuple val(meta), path("*.ann.tab") , optional:true, emit: tab
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tuple val(meta), path("*.ann.json") , optional:true, emit: json
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path "*.summary.html" , emit: report
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
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def prefix = task.ext.prefix ?: "${meta.id}"
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def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
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def reference = fasta ? "--fasta $fasta" : ""
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"""
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mkdir $prefix
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vep \\
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-i $vcf \\
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-o ${prefix}.ann.vcf \\
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-o ${prefix}.ann.${file_extension} \\
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$args \\
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$reference \\
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--assembly $genome \\
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@ -44,10 +45,8 @@ process ENSEMBLVEP {
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--cache_version $cache_version \\
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--dir_cache $dir_cache \\
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--fork $task.cpus \\
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--vcf \\
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--stats_file ${prefix}.summary.html
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--stats_file ${prefix}.summary.html \\
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rm -rf $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -1,5 +1,5 @@
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name: ENSEMBLVEP
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description: Ensembl Variant Effect Predictor (VEP)
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description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`.
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keywords:
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- annotation
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tools:
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@ -49,8 +49,18 @@ output:
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- vcf:
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type: file
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description: |
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annotated vcf
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annotated vcf (optional)
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pattern: "*.ann.vcf"
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- tab:
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type: file
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description: |
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tab file with annotated variants (optional)
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pattern: "*.ann.tab"
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- json:
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type: file
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description: |
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json file with annotated variants (optional)
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pattern: "*.ann.json"
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- report:
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type: file
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description: VEP report file
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@ -4,6 +4,43 @@ nextflow.enable.dsl = 2
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include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/ensemblvep/main.nf'
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include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/ensemblvep/main.nf'
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workflow test_ensemblvep_fasta_json {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_tab {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_vcf {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta {
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input = [
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[ id:'test' ], // meta map
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@ -6,4 +6,18 @@ process {
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container = 'nfcore/vep:104.3.WBcel235'
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}
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withName: ENSEMBLVEP_JSON {
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container = 'nfcore/vep:104.3.WBcel235'
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ext.args = '--json'
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}
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withName: ENSEMBLVEP_TAB {
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container = 'nfcore/vep:104.3.WBcel235'
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ext.args = '--tab'
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}
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withName: ENSEMBLVEP_VCF {
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container = 'nfcore/vep:104.3.WBcel235'
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ext.args = '--vcf'
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}
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}
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@ -1,5 +1,29 @@
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- name: ensemblvep test_ensemblvep_fasta_json
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.json
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_fasta_tab
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.tab
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_fasta_vcf
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.vcf
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_fasta
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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@ -7,7 +31,7 @@
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_no_fasta
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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