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nf-cmgg-testdata.config
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nf-cmgg-testdata.config
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// Base directory for test data
def test_data_dir = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/"
params {
test_data {
'homo_sapiens' {
'genome' {
genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna"
genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.fna.fai"
genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.dict"
genome_sdf = "${test_data_dir}/genomics/homo_sapiens/genome/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21_sdf.tar.gz"
genome_strtablefile = "${test_data_dir}/genomics/homo_sapiens/genome/gatk4/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set_chr21.str.zip"
genome_qdnaseq = "${test_data_dir}/genomics/homo_sapiens/genome/qdnaseq/chr21.10kbp.rda"
bowtie2 = "${test_data_dir}/genomics/homo_sapiens/genome/bowtie2.tar.gz"
bwa = "${test_data_dir}/genomics/homo_sapiens/genome/bwa.tar.gz"
bwamem2 = "${test_data_dir}/genomics/homo_sapiens/genome/bwamem2.tar.gz"
dragmap = "${test_data_dir}/genomics/homo_sapiens/genome/dragmap.tar.gz"
snapaligner = "${test_data_dir}/genomics/homo_sapiens/genome/snapaligner.tar.gz"
expansionhunter = "${test_data_dir}/genomics/homo_sapiens/genome/expansionhunter/variant_catalog.json"
}
'illumina' {
genelists = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/genelists.tar.gz"
test_fastq_R1 = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_R1.fastq.gz"
test_fastq_R2 = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_R2.fastq.gz"
test_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.bam"
test_bam_index = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.bam.bai"
test_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.cram"
test_cram_index = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.cram.crai"
test2_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.cram"
test2_cram_index = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.cram.crai"
test_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.vcf.gz"
test_vcf_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi"
test2_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz"
test2_vcf_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz.tbi"
test_gvcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.g.vcf.gz"
test_gvcf_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.g.vcf.gz.tbi"
test2_gvcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test2.g.vcf.gz"
test2_gvcf_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test2.g.vcf.gz.tbi"
test_per_base = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/test.per-base.bed.gz"
test_per_base_index = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/test.per-base.bed.gz.csi"
test_quantized_bed = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/test.quantized.bed.gz"
test2_quantized_bed = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/test2.quantized.bed.gz"
roi_bed = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/roi.bed"
roi_intervals = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/roi.interval_list"
test_sv_Poscon1_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon1.cram"
test_sv_Poscon1_cram_index = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon1.cram.crai"
test_sv_Poscon1_roi = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/SVcontrol/PosCon1and2.roi.bed"
test_sv_Poscon2_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon2.cram"
test_sv_Poscon2_cram_index = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon2.cram.crai"
test_sv_Poscon2_roi = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/SVcontrol/PosCon1and2.roi.bed"
test_sv_Poscon3_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon3.cram"
test_sv_Poscon3_cram_index = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon3.cram.crai"
test_sv_Poscon3_roi = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/SVcontrol/PosCon3.roi.bed"
test_sv_Poscon4_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon4.cram"
test_sv_Poscon4_cram_index = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/SVcontrol/PosCon4.cram.crai"
test_sv_Poscon4_roi = "${test_data_dir}/genomics/homo_sapiens/illumina/regions/SVcontrol/PosCon4.roi.bed"
}
}
}
}