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add in testdata paths

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Rike 2022-05-22 13:35:35 +02:00
parent 5d72500d60
commit cd60b4c6eb
2 changed files with 16 additions and 27 deletions
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38
tests/modules/gatk4/filtervarianttranches/main.nf
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@ -3,36 +3,24 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf' include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf'
include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf'
include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf'
workflow test_gatk4_filtervarianttranches { workflow test_gatk4_filtervarianttranches {
resources = [ file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ]
resources_index = [
file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true),
]
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
[] []
] ]
resources = [ fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
//file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true), dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
//file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
//file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
]
resources_index =[ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
//file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
//file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
//file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
]
// , [
// 'hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
// 'omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
// '1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
// 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
// ]]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) GATK4_FILTERVARIANTTRANCHES (input , resources, resources_index, fasta, fai, dict)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
GATK4_FILTERVARIANTTRANCHES ( input, resources, resources_index, fasta, fai, dict)
} }

5
tests/modules/gatk4/filtervarianttranches/nextflow.config
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@ -1,5 +1,6 @@
process { process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
} ext.args = "--info-key CNN_1D"
}