// Base directory for test data
def test_data_dir = "${launchDir}/tests/data/"

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"

                test_wig_gz                               = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.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"
                
                contigs_fasta                             = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta"
            }
            'illumina' {
                test_single_end_bam                       = "${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_baserecalibrator_table               = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"

                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                          = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
            }
            'nanopore' {
                test_sorted_bam                           = "${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_fastq_gz                             = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"

                test_sequencing_summary                   = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
            }
        }
        'homo_sapiens' {
            'illumina' {
                test_paired_end_bam                       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
            }
        }
    }
}