mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
17fbdf96cb
* Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
70 lines
5.9 KiB
Text
70 lines
5.9 KiB
Text
// Base directory for test data
|
|
def test_data_dir = "${launchDir}/tests/data/"
|
|
|
|
params {
|
|
test_data {
|
|
'sarscov2' {
|
|
'genome' {
|
|
genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
|
|
genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
|
|
genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
|
|
genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
|
|
genome_gtf = "${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"
|
|
}
|
|
'illumina' {
|
|
test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"
|
|
test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam"
|
|
test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam.bai"
|
|
test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.bam"
|
|
test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam"
|
|
test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai"
|
|
test_methylated_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam"
|
|
test_methylated_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam"
|
|
test_methylated_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai"
|
|
test_unaligned_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_unaligned.bam"
|
|
|
|
test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
|
|
test_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
|
|
test2_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
|
|
test2_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
|
|
test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz"
|
|
test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz"
|
|
|
|
test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
|
|
|
|
test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
|
|
test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
|
|
test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
|
|
test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf"
|
|
test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
|
|
test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
|
|
test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
|
|
test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
|
|
test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
|
|
}
|
|
'nanopore' {
|
|
test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"
|
|
test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai"
|
|
|
|
test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
|
|
}
|
|
}
|
|
'homo_sapiens' {
|
|
'illumina' {
|
|
test_paired_end_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
|
|
}
|
|
}
|
|
}
|
|
}
|