// Base directory for test data
def test_data_dir = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/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_paf                                     = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
                genome_sizes                                   = "${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"

                ncbi_taxmap_zip                                = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
                taxon_list_txt                                 = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"

                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_genome_maf_gz                          = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz"
                contigs_genome_par                             = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/contigs.genome.par"
                lastdb_tar_gz                                  = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz"

                baits_interval_list                            = "${test_data_dir}/genomics/sarscov2/genome/picard/baits.interval_list"
                targets_interval_list                          = "${test_data_dir}/genomics/sarscov2/genome/picard/targets.interval_list"
            }
            '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_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_bcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf"

                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"
                test2_vcf_targets_tsv_gz                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz"
                test3_vcf                                      = "${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                                   = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
                assembly_gfa_bgz                               = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz"
                assembly_gfa_gz                                = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.gz"
                assembly_gfa_zst                               = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.zst"

                test_single_end_bam_readlist_txt               = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"

                SRR13255544_tar_gz                             = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
                SRR11140744_tar_gz                             = "${test_data_dir}/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
            }
            '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"

                fast5_tar_gz                                   = "${test_data_dir}/genomics/sarscov2/nanopore/fast5/fast5.tar.gz"

                test_fastq_gz                                  = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"

                test_sequencing_summary                        = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
            }
        }
        'homo_sapiens' {
            'genome' {
                genome_fasta                                   = "${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_interval_list                           = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
                genome_sizes                                   = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
                genome_bed                                     = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
                genome_header                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
                genome_bed_gz                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz"
                genome_bed_gz_tbi                              = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
                transcriptome_fasta                            = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
                genome2_fasta                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
                genome_chain_gz                                = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
                genome_21_fasta                                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
                genome_21_fasta_fai                            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
                genome_21_dict                                 = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
                genome_21_sizes                                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
                genome_21_interval_list                        = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
                genome_21_multi_interval_bed                   = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
                genome_21_multi_interval_bed_gz                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
                genome_21_multi_interval_bed_gz_tbi            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
                genome_21_chromosomes_dir                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"

                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"
                syntheticvcf_short_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
                syntheticvcf_short_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
                syntheticvcf_short_score                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
                gnomad_r2_1_1_sv_vcf_gz                        = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"

                hapmap_3_3_hg38_21_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
                hapmap_3_3_hg38_21_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
                res_1000g_omni2_5_hg38_21_vcf_gz               = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz"
                res_1000g_omni2_5_hg38_21_vcf_gz_tbi           = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi"
                res_1000g_phase1_snps_hg38_21_vcf_gz           = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz"
                res_1000g_phase1_snps_hg38_21_vcf_gz_tbi       = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi"
                dbsnp_138_hg38_21_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
                dbsnp_138_hg38_21_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
                gnomad_r2_1_1_21_vcf_gz                        = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
                gnomad_r2_1_1_21_vcf_gz_tbi                    = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
                mills_and_1000g_indels_21_vcf_gz               = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
                mills_and_1000g_indels_21_vcf_gz_tbi           = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"

                index_salmon                                   = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
                repeat_expansions                              = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
                justhusky_ped                                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
                justhusky_minimal_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
                justhusky_minimal_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"

                vcfanno_tar_gz                                 = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
                vcfanno_toml                                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
            }
            'pangenome' {
                pangenome_fa                                  = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
                pangenome_fa_gz                               = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
                pangenome_paf                                 = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
                pangenome_paf_gz                              = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
                pangenome_seqwish_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
                pangenome_smoothxg_gfa                        = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
                pangenome_gfaffix_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
                'odgi' {
                    pangenome_og                                  = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
                    pangenome_lay                                 = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
                }
            }
            'illumina' {
                test_paired_end_sorted_bam                              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
                test_paired_end_sorted_bam_bai                          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
                test_paired_end_name_sorted_bam                         = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam"
                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_markduplicates_sorted_referencesn_txt   = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
                test_paired_end_recalibrated_sorted_bam                 = "${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                 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
                test_paired_end_hla                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
                test_paired_end_hla_sorted_bam                          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
                test_paired_end_hla_sorted_bam_bai                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
                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_name_sorted_bam               = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
                test2_paired_end_markduplicates_sorted_bam     = "${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"


                mitochon_standin_recalibrated_sorted_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
                mitochon_standin_recalibrated_sorted_bam_bai   = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"

                test_paired_end_sorted_cram                      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
                test_paired_end_sorted_cram_crai                 = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
                test_paired_end_markduplicates_sorted_cram       = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
                test_paired_end_markduplicates_sorted_cram_crai  = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
                test_paired_end_recalibrated_sorted_cram         = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
                test_paired_end_recalibrated_sorted_cram_crai    = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"

                test2_paired_end_sorted_cram                     = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
                test2_paired_end_sorted_cram_crai                = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
                test2_paired_end_markduplicates_sorted_cram      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
                test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
                test2_paired_end_recalibrated_sorted_cram        = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
                test2_paired_end_recalibrated_sorted_cram_crai   = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"

                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_rnaseq_1_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz"
                test_rnaseq_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_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_pileups_table                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
                test2_pileups_table                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"

                test_genomicsdb_tar_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
                test_pon_genomicsdb_tar_gz                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"

                test2_haplotc_ann_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
                test2_haplotc_ann_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"

                test2_recal                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
                test2_recal_idx                                = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
                test2_tranches                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
                test2_allele_specific_recal                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
                test2_allele_specific_recal_idx                = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
                test2_allele_specific_tranches                 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"

                test_test2_paired_mutect2_calls_vcf_gz         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
                test_test2_paired_mutect2_calls_vcf_gz_tbi     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
                test_test2_paired_mutect2_calls_vcf_gz_stats   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
                test_test2_paired_mutect2_calls_f1r2_tar_gz    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
                test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
                test_test2_paired_segmentation_table           = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
                test_test2_paired_contamination_table          = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.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"

                test_genome21_indels_vcf_gz                    = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
                test_genome21_indels_vcf_gz_tbi                = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"

                test_mpileup                                   = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
                test2_mpileup                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"

                test_broadpeak                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
                test2_broadpeak                                = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"

                test_narrowpeak                                = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
                test2_narrowpeak                               = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"

                test_10x_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
                test_10x_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"

                test_yak                                      = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
                test2_yak                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"

                cutandrun_bedgraph_test_1                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
                cutandrun_bedgraph_test_2                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"

                test_rnaseq_vcf                               =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
                test_sv_vcf                                   =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"

                test_pytor                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
            }
            'pacbio' {
                primers                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
                alz                                           = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
                alzpbi                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
                ccs                                           = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
                ccs_fa                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
                ccs_fa_gz                                     = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
                ccs_fq                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
                ccs_fq_gz                                     = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
                ccs_xml                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
                hifi                                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
                lima                                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
                refine                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
                cluster                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
                singletons                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
                aligned                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
                alignedbai                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
                genemodel1                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
                genemodel2                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
                filelist                                      = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
            }
        }
        'bacteroides_fragilis' {
            'genome' {
                genome_fna_gz                   = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
                genome_paf                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
                genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"

            }
            'illumina' {
                test1_contigs_fa_gz             = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
                test1_1_fastq_gz                = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
                test1_2_fastq_gz                = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
                test2_1_fastq_gz                = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
                test2_2_fastq_gz                = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
                test1_paired_end_bam            = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam"
                test1_paired_end_sorted_bam     = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
                test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
                test2_paired_end_bam            = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam"
                test2_paired_end_sorted_bam     = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
                test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
            }
            'nanopore' {
                test_fastq_gz                   = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
                overlap_paf                     = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf"
            }
        }
        'candidatus_portiera_aleyrodidarum' {
            'genome' {
                genome_fasta                    = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta"
                genome_sizes                    = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes"
                genome_aln_gz                   = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz"
                genome_aln_nwk                  = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk"
                proteome_fasta                  = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta"
                test1_gff                       = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff"
                test2_gff                       = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff"
                test3_gff                       = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
            }
            'illumina' {
                test_1_fastq_gz                 = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fasta/test_1.fastq.gz"
                test_2_fastq_gz                 = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
                test_se_fastq_gz                = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
            }
            'nanopore' {
                test_fastq_gz                   = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz"
            }
        }
        'haemophilus_influenzae' {
            'genome' {
                genome_fna_gz                   = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz"
                genome_aln_gz                   = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz"
                genome_aln_nwk                  = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk"
            }
        }
        'generic' {
            'csv' {
                test_csv = "${test_data_dir}/generic/csv/test.csv"
            }
            'notebooks' {
                rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
                ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
                ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
            }
            'tsv' {
                test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
            }
            'txt' {
                hello = "${test_data_dir}/generic/txt/hello.txt"
            }
            'cnn' {
                 reference = "${test_data_dir}/generic/cnn/reference.cnn"
            }
            'cooler'{
                test_pairix_pair_gz                           = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
                test_pairix_pair_gz_px2                       = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
                test_pairs_pair                               = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
                test_tabix_pair_gz                            = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
                test_tabix_pair_gz_tbi                        = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
                hg19_chrom_sizes                              = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
                test_merge_cool                               = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
                test_merge_cool_cp2                           = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"

            }
        }
    }
}