// 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 = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta" proteome_fasta = "${test_data_dir}/genomics/sarscov2/genome/proteome.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" kraken2_bracken = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken" kraken2_bracken_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" kaiju = "${test_data_dir}/genomics/sarscov2/genome/db/kaiju" kaiju_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kaiju.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 = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" } 'metagenome' { classified_reads_assignment = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" kraken_report = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" krona_taxonomy = "${test_data_dir}/genomics/sarscov2/metagenome/krona_taxonomy.tab" } } 'homo_sapiens' { 'genome' { genome_elfasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elfasta" genome_fasta = "${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 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list" genome_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.multi_intervals.bed" 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 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi" genome_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elsites" 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_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" dbsnp_146_hg38_vcf_gz = "${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 = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" gnomad2_r2_1_1_sv_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD2.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" haplotype_map = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" index_salmon = "${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 = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.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" } } } }