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https://github.com/MillironX/nf-core_modules.git
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Add indices and meta
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Rike
parent
15fba1dd7c
commit
5ae757121f
3 changed files with 73 additions and 36 deletions
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@ -8,16 +8,17 @@ process GATK4_FILTERVARIANTTRANCHES {
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(intervals)
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path ressources
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tuple val(meta), path(vcf), path(tbi),path(intervals)
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path resources
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path resources_index
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path fasta
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path fai
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path dict
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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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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@ -26,7 +27,7 @@ process GATK4_FILTERVARIANTTRANCHES {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def ressources = ressources.collect{"--ressources $it"}.join(' ')
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def resources = resources.collect{"--resource $it"}.join(' ')
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK FilterVariantTranches] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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@ -36,7 +37,7 @@ process GATK4_FILTERVARIANTTRANCHES {
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"""
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gatk --java-options "-Xmx${avail_mem}g" FilterVariantTranches \\
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--variant $vcf \\
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$ressources \\
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$resources \\
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--output ${prefix}.filtered.vcf.gz \\
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--tmp-dir . \\
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$args
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@ -1,51 +1,64 @@
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name: "gatk4_filtervarianttranches"
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## TODO nf-core: Add a description of the module and list keywords
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description: write your description here
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description: Apply tranche filtering
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keywords:
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- sort
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- gatk4
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- filtervarianttranches
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tools:
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- "gatk4":
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## TODO nf-core: Add a description and other details for the software below
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description: "Genome Analysis Toolkit (GATK4)"
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homepage: "None"
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documentation: "None"
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tool_dev_url: "https://github.com/broadinstitute/gatk"
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doi: ""
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licence: "['BSD-3-clause']"
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description: Genome Analysis Toolkit (GATK4)
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us
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tool_dev_url: https://github.com/broadinstitute/gatk
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doi: "10.1158/1538-7445.AM2017-3590"
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licence: ["BSD-3-clause"]
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## TODO nf-core: Add a description of all of the variables used as input
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input:
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# Only when we have meta
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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#
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## TODO nf-core: Delete / customise this example input
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- bam:
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- vcf:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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description: a VCF file containing variants, must have info key:CNN_2D
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: tbi file matching with -vcf
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pattern: "*.vcf.gz.tbi"
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- resources:
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type: list
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description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
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pattern: "*.vcf.gz"
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- resources_index:
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type: list
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description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
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pattern: "*.vcf.gz"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "fasta.fai"
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- dict:
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## TODO nf-core: Add a description of all of the variables used as output
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output:
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#Only when we have meta
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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#
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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## TODO nf-core: Delete / customise this example output
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- bam:
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- vcf:
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type: file
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description: Sorted BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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description: VCF file
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pattern: "*.vcf.gz"
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authors:
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- "@FriederikeHanssen"
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@ -5,11 +5,34 @@ nextflow.enable.dsl = 2
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include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf'
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workflow test_gatk4_filtervarianttranches {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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GATK4_FILTERVARIANTTRANCHES ( input )
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
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[]
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]
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resources = [
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file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
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//file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true),
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//file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
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//file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
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]
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resources_index =[ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
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//file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
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//file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
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//file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
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]
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// , [
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// 'hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
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// 'omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
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// '1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
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// 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
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// ]]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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GATK4_FILTERVARIANTTRANCHES ( input, resources, resources_index, fasta, fai, dict)
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}
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