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Add gvcf index files (#472)

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FriederikeHanssen 2021-04-28 21:23:10 +02:00 committed by GitHub
parent 9b0aa3e239
commit 9ce4427275
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1 changed files with 19 additions and 12 deletions
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31
tests/config/test_data.config
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@ -14,16 +14,16 @@ params {
genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"
test_bed_gz = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed.gz"
test2_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test2.bed"
test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
}
@ -38,24 +38,24 @@ params {
test_paired_end_methylated_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam"
test_paired_end_methylated_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai"
test_unaligned_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.unaligned.bam"
test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
test2_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz"
test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz"
test_bedgraph = "${test_data_dir}/genomics/sarscov2/illumina/bedgraph/test.bedgraph"
test_bigwig = "${test_data_dir}/genomics/sarscov2/illumina/bigwig/test.bigwig"
test_wig_gz = "${test_data_dir}/genomics/sarscov2/illumina/wig/test.wig.gz"
test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
@ -65,10 +65,10 @@ params {
test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
contigs_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/contigs.fasta"
scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
}
'nanopore' {
@ -137,7 +137,14 @@ params {
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
}
}
}