// 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_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                                  = "${test_data_dir}/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz"
            }
            'illumina' {
                test_single_end_bam                            = "${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_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"

                test_single_end_bam_readlist_txt               = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
            }
            'nanopore' {
                test_sorted_bam                                = "${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_sizes                                   = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
                genome_bed                                     = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
                transcriptome_fasta                            = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
                genome2_fasta                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"

                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"
                index_salmon                                   = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
                repeat_expansions                              = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
            }
            '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_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_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_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_10x_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_1.fastq.gz"
                test_10x_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_2.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"
            }
            '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                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
                genemodel2                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
            }
        }
    }
}