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test_data.config
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test_data.config
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// Base directory for test data
params {
test_data {
'sarscov2' {
'genome' {
genome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta"
genome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz"
genome_fasta_fai = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai"
genome_dict = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.dict"
genome_gff3 = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3"
genome_gff3_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz"
genome_gtf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gtf"
genome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.paf"
genome_sizes = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta"
proteome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta"
transcriptome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf"
test_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed"
test_bed_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz"
test2_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed"
test_bed12 = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12"
baits_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed"
bed_autosql = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as"
reference_cnn = "${params.test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn"
kraken2 = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2"
kraken2_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz"
kraken2_bracken = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken"
kraken2_bracken_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz"
kaiju = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju"
kaiju_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz"
kofamscan_profiles_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz"
kofamscan_ko_list_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz"
ncbi_taxmap_zip = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
taxon_list_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
mmseqs_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz"
all_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas"
contigs_genome_maf_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz"
contigs_genome_par = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par"
lastdb_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz"
baits_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list"
targets_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list"
}
'illumina' {
test_single_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam"
test_single_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam"
test_single_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai"
test_paired_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam"
test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam"
test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai"
test_paired_end_methylated_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam"
test_paired_end_methylated_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam"
test_paired_end_methylated_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai"
test_unaligned_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam"
test_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
test_interleaved_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz"
test2_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
test_methylated_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz"
test_methylated_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz"
test_bedgraph = "${params.test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph"
test_bigwig = "${params.test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig"
test_wig_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz"
test_baserecalibrator_table = "${params.test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
test_computematrix_mat_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
test_bcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf"
test_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf"
test_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz"
test_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
test2_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf"
test2_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
test2_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
test2_vcf_targets_tsv_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz"
test3_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf"
test3_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
test3_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
contigs_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta"
scaffolds_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
assembly_gfa = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa"
assembly_gfa_bgz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz"
assembly_gfa_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz"
assembly_gfa_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst"
test_single_end_bam_readlist_txt = "${params.test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz"
SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz"
}
'nanopore' {
test_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam"
test_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai"
fast5_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz"
test_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
test_sequencing_summary = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
}
'metagenome' {
classified_reads_assignment = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt"
kraken_report = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
krona_taxonomy = "${params.test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab"
seqid2taxid_map = "${params.test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map"
}
}
'mus_musculus' {
'genome' {
rnaseq_samplesheet = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv"
rnaseq_genemeta = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv"
rnaseq_contrasts = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv"
rnaseq_matrix = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv"
deseq_results = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv"
}
}
'homo_sapiens' {
'genome' {
genome_elfasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta"
genome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta"
genome_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai"
genome_strtablefile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip"
genome_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict"
genome_gff3 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3"
genome_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf"
genome_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list"
genome_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
genome_blacklist_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed"
genome_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes"
genome_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed"
genome_header = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.header"
genome_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz"
genome_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
genome_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites"
transcriptome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta"
genome2_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta"
genome_chain_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz"
genome_annotated_interval_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv"
genome_preprocessed_count_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv"
genome_preprocessed_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list"
genome_21_sdf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz"
genome_21_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
genome_21_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
genome_21_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
genome_21_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
genome_21_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
genome_21_annotated_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed"
genome_21_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
genome_21_multi_interval_antitarget_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed"
genome_21_multi_interval_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
genome_21_multi_interval_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
genome_21_chromosomes_dir = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
genome_21_reference_cnn = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn"
genome_21_eigenstrat_snp = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp"
dbsnp_146_hg38_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
dbsnp_146_hg38_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
dbsnp_146_hg38_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
gnomad_r2_1_1_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
gnomad_r2_1_1_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
mills_and_1000g_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
mills_and_1000g_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
syntheticvcf_short_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
syntheticvcf_short_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
syntheticvcf_short_score = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
gnomad_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
gnomad2_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz"
hapmap_3_3_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
hapmap_3_3_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"
res_1000g_omni2_5_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz"
res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi"
res_1000g_phase1_snps_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz"
res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi"
dbsnp_138_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz"
dbsnp_138_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi"
gnomad_r2_1_1_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz"
gnomad_r2_1_1_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
mills_and_1000g_indels_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
mills_and_1000g_indels_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
haplotype_map = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt"
ngscheckmate_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
index_salmon = "${params.test_data_base}/data/genomics/homo_sapiens/genome/index/salmon"
repeat_expansions = "${params.test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
justhusky_ped = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
justhusky_minimal_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
justhusky_minimal_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
vcfanno_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
vcfanno_toml = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
vep_cache = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz"
}
'pangenome' {
pangenome_fa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa"
pangenome_fa_bgzip = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz"
pangenome_fa_bgzip_fai = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai"
pangenome_fa_bgzip_gzi = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi"
pangenome_paf = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf"
pangenome_paf_gz = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz"
pangenome_seqwish_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
pangenome_smoothxg_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
pangenome_gfaffix_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
'odgi' {
pangenome_og = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og"
pangenome_lay = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay"
}
}
'illumina' {
test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
test_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam"
test_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
test_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
test_paired_end_markduplicates_sorted_referencesn_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
test_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam"
test_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai"
test_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam"
test_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam"
test_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam"
test_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
test_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
test_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
test_paired_end_hla = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
test_paired_end_hla_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
test_paired_end_hla_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
test_rna_paired_end_sorted_chr6_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam"
test_rna_paired_end_sorted_chr6_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai"
test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
test2_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
test2_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
test2_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
test2_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
test2_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
test2_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
test2_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
test2_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
test2_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
test2_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
test2_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
test_paired_end_duplex_umi_unmapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam"
test_paired_end_duplex_umi_mapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam"
test_paired_end_duplex_umi_mapped_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam"
test_paired_end_duplex_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam"
test_paired_end_duplex_umi_duplex_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam"
mitochon_standin_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
mitochon_standin_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
test3_single_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
read_group_settings_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt"
test_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
test_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
test_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
test_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
test_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
test_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
test2_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
test2_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
test2_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
test2_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
test2_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
test2_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
test_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
test_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
test_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
test2_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
test2_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
test2_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
test_rnaseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
test_rnaseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
test_paired_end_duplex_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz"
test_paired_end_duplex_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz"
test_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
test2_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
test_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
test2_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
test_paired_end_sorted_dragstrmodel = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
test_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
test_pon_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
test2_haplotc_ann_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
test2_haplotc_ann_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
test_haplotc_cnn_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz"
test_haplotc_cnn_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi"
test2_haplotc_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz"
test2_haplotc_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi"
test2_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
test2_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
test2_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
test2_allele_specific_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
test2_allele_specific_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
test2_allele_specific_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
test_test2_paired_mutect2_calls_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
test_test2_paired_mutect2_calls_vcf_gz_stats = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${params.test_data_base}/data/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 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
test_test2_paired_segmentation_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
test_test2_paired_contamination_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
test_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
test_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
test_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
test_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
test_genome_vcf_ud = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD"
test_genome_vcf_mu = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu"
test_genome_vcf_bed = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed"
test2_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
test2_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
test2_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
test2_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
test_genome21_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
test_genome21_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
test_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
test2_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
test_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
test2_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
test_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
test2_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
test_10x_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
test_10x_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
test_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak"
test2_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak"
cutandrun_bedgraph_test_1 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
cutandrun_bedgraph_test_2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
test_rnaseq_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
test_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
genmod_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz"
genmod_annotate_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz"
genmod_models_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz"
genmod_score_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz"
test_mito_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz"
test_pytor = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor"
rank_model = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini"
test_flowcell = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
test_flowcell_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv"
contig_ploidy_priors_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
}
'pacbio' {
primers = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
alz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam"
alzpbi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
ccs = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
ccs_fa = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
ccs_fa_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
ccs_fq = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
ccs_fq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
ccs_xml = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
hifi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
lima = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
refine = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
cluster = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
singletons = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
aligned = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
alignedbai = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
genemodel1 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
genemodel2 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
filelist = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt"
}
'scramble' {
fasta = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa"
fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai"
bam = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam"
bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai"
cram = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram"
cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai"
bed = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bed"
}
'gene_set_analysis' {
gct = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct"
cls = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls"
gmx = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx"
}
'cnvkit' {
amplicon_cnr = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr"
amplicon_cns = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns"
}
}
'bacteroides_fragilis' {
'genome' {
genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
genome_gbff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
genome_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
genome_gff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz"
}
'hamronization' {
genome_abricate_tsv = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv"
genome_mapping_potential_arg = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG"
}
'illumina' {
test1_contigs_fa_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
test1_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
test1_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
test2_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
test1_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam"
test1_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
test1_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
test2_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam"
test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
}
'nanopore' {
test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
overlap_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf"
}
}
'candidatus_portiera_aleyrodidarum' {
'genome' {
genome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta"
genome_sizes = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes"
genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz"
genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk"
proteome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta"
test1_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff"
test2_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff"
test3_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
}
'illumina' {
test_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
test_se_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
}
'nanopore' {
test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz"
}
}
'haemophilus_influenzae' {
'genome' {
genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz"
genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz"
genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk"
}
}
'generic' {
'csv' {
test_csv = "${params.test_data_base}/data/generic/csv/test.csv"
}
'notebooks' {
rmarkdown = "${params.test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
ipython_md = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md"
ipython_ipynb = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb"
}
'tar' {
tar_gz = "${params.test_data_base}/data/generic/tar/hello.tar.gz"
}
'tsv' {
test_tsv = "${params.test_data_base}/data/generic/tsv/test.tsv"
}
'txt' {
hello = "${params.test_data_base}/data/generic/txt/hello.txt"
}
'cooler'{
test_pairix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
test_pairix_pair_gz_px2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
test_pairs_pair = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
test_tabix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
test_tabix_pair_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
hg19_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
test_merge_cool = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
test_merge_cool_cp2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
}
'config' {
ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg"
}
}
'proteomics' {
'msspectra' {
ups_file1 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw"
ups_file2 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw"
}
'database' {
yeast_ups = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta"
}
'parameter' {
maxquant = "${params.test_data_base}/data/proteomics/parameter/mqpar.xml"
}
'idfile' {
openms_idxml = "${params.test_data_base}/data/proteomics/openms_idxml/BSA_QC_file.idXML"
}
}
'mus_musculus' {
'illumina' {
test_1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz"
test_2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz"
}
'csv' {
count_table = "${params.test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv"
library = "${params.test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv"
}
'txt' {
design_matrix = "${params.test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt"
}
}
'galaxea_fascicularis' {
hic {
pretext = "${params.test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext"
}
}
}
}