mirror of
https://github.com/MillironX/nf-core_modules.git
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83a500e6b0
* Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint * Initial commit for test data config * Rename test data * Include test config * Update indents * Update test for FastQC via config * Remove quotes of bottom-level variables * Use underscores in key names * Get tests working for fastp * Remove whitespace at beginning of file
69 lines
No EOL
5.9 KiB
Text
69 lines
No EOL
5.9 KiB
Text
// Base directory for test data
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def test_data_dir = "${launchDir}/tests/data/"
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params {
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test_data {
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'sarscov2' {
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'genome' {
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genome_fasta = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
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genome_fasta_fai = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
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genome_dict = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
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genome_gff3 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
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genome_gtf = "${test_data_dir}/genomics/sarscov2/genome/genome.gtf"
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genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
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transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
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transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
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test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"
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test_bed_gz = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed.gz"
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test2_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test2.bed"
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test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
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baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
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kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
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}
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'illumina' {
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test_single_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"
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test_single_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam"
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test_single_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.sorted.bam.bai"
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test_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.bam"
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test_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam"
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test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai"
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test_methylated_paired_end_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.bam"
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test_methylated_paired_end_sorted_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam"
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test_methylated_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_methylated_paired_end.sorted.bam.bai"
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test_unaligned_bam = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_unaligned.bam"
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test_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_1.fastq.gz"
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test_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_2.fastq.gz"
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test2_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz"
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test2_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz"
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test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz"
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test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz"
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test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table"
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test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
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test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
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test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
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test2_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf"
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test2_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz"
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test2_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi"
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test3_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf"
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test3_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz"
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test3_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi"
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}
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'nanopore' {
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test_sorted_bam = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"
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test_sorted_bam_bai = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai"
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test_fastq_gz = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
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}
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}
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'homo_sapiens' {
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'illumina' {
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test_paired_end_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
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}
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}
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}
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} |