From ae154b8c3f29b6d8d57d92286b8c643fc744ba20 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 19 Apr 2021 16:30:43 +0200 Subject: [PATCH] Add human data paths (#458) * Add new human data and fix sarscov paths * Fix filename typo * Apply code review * replace index with to match sarscov data * lower case * indent everythin * Adapt sarscov keys to new naming convention * Update test_data.config Co-authored-by: Harshil Patel --- tests/config/test_data.config | 188 ++++++++++++++++++++++------------ 1 file changed, 123 insertions(+), 65 deletions(-) diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 2a979881..b7262e09 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -5,81 +5,139 @@ params { test_data { 'sarscov2' { 'genome' { - genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta" - genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai" - genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict" - genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3" - genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz" - genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf" - 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" + genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta" + genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai" + genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict" + genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3" + genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz" + genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf" + 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" } 'illumina' { - test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam" - test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam" - test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam.bai" - test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.bam" - test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam" - test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai" - test_methylated_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam" - test_methylated_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam" - test_methylated_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai" - test_unaligned_bam = "${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" - test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf" - test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz" - test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" - test3_vcf = "${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 = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa" + test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.bam" + test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" + test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" + test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.bam" + test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_methylated_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" + 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 = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" + test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf" + test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz" + test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" + 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' { - test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam" - test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" + test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam" + test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" - test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz" + test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz" - test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" + test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" } } 'homo_sapiens' { + 'genome' { + genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta" + genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai" + genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict" + genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3" + genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf" + genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes" + genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed" + + dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + gnomad_r2_1_1_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + } 'illumina' { - test_paired_end_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam" + test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" + test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" + test_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" + test_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" + test_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" + test_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" + test_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" + test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" + test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" + test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" + + test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" + test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" + test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" + test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" + test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" + test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" + test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" + test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" + test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" + test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" + test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" + test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" + + test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" + test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" + test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" + test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" + test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" + test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" + + test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" + test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" + + test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" + test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" } } }