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https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Fix some module tests after switching to config data (#386)
* 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
This commit is contained in:
parent
1e4fa57139
commit
17fbdf96cb
7 changed files with 89 additions and 84 deletions
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@ -1,69 +1,70 @@
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// 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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
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}
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}
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}
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}
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// Base directory for test data
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def test_data_dir = "${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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kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
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}
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'illumina' {
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test_single_end_bam = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
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}
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}
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}
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}
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BIN
tests/data/genomics/sarscov2/genome/db/kraken2.tar.gz
Normal file
BIN
tests/data/genomics/sarscov2/genome/db/kraken2.tar.gz
Normal file
Binary file not shown.
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@ -6,8 +6,8 @@ include { CAT_FASTQ } from '../../../../software/cat/fastq/main.nf' addParams( o
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workflow test_cat_fastq_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true) ]
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
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]
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CAT_FASTQ ( input )
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workflow test_cat_fastq_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz", checkIfExists: true) ]
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
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]
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CAT_FASTQ ( input )
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@ -6,19 +6,19 @@ include { KRAKEN2_RUN } from '../../../../software/kraken2/run/main.nf' addParam
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workflow test_kraken2_run_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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db = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/db/kraken2", checkIfExists: true) ]
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db = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
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KRAKEN2_RUN ( input, db )
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}
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workflow test_kraken2_run_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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db = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/db/kraken2", checkIfExists: true) ]
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db = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
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KRAKEN2_RUN ( input, db )
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}
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- path: output/kraken2/test.unclassified_2.fastq.gz
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should_exist: true
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- path: output/kraken2/test.kraken2.report.txt
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md5sum: 5fb165fd0bdf920ff6cf6f734371a4cf
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md5sum: 4227755fe40478b8d7dc8634b489761e
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
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include { UNTAR } from '../../../software/untar/main.nf' addParams( options: [:] )
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workflow test_untar {
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input = file("${launchDir}/tests/data/generic/test.txt.tar.gz", checkIfExists: true)
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input = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
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UNTAR ( input )
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}
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@ -3,5 +3,9 @@
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tags:
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- untar
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files:
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- path: output/untar/test.txt
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md5sum: 7171d4ec2ad0882fab4b0142536d93a1
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- path: output/untar/kraken2/hash.k2d
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md5sum: 8b8598468f54a7087c203ad0190555d9
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- path: output/untar/kraken2/opts.k2d
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md5sum: a033d00cf6759407010b21700938f543
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- path: output/untar/kraken2/taxo.k2d
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md5sum: 094d5891cdccf2f1468088855c214b2c
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