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Fix some module tests after switching to config data (#386)

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* 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:
Jose Espinosa-Carrasco 2021-03-24 19:28:07 +01:00 committed by GitHub
parent 1e4fa57139
commit 17fbdf96cb
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7 changed files with 89 additions and 84 deletions
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139
tests/config/test_data.config
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@ -1,69 +1,70 @@
// 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 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
}
'illumina' {
test_single_end_bam = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
}
}
}
}
// Base directory for test data
def test_data_dir = "${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"
}
}
}
}

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tests/data/genomics/sarscov2/genome/db/kraken2.tar.gz Normal file
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12
tests/software/cat/fastq/main.nf
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@ -6,8 +6,8 @@ include { CAT_FASTQ } from '../../../../software/cat/fastq/main.nf' addParams( o
workflow test_cat_fastq_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
]
CAT_FASTQ ( input )
@ -15,10 +15,10 @@ workflow test_cat_fastq_single_end {
workflow test_cat_fastq_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
]
CAT_FASTQ ( input )

10
tests/software/kraken2/run/main.nf
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@ -6,19 +6,19 @@ include { KRAKEN2_RUN } from '../../../../software/kraken2/run/main.nf' addParam
workflow test_kraken2_run_single_end {
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
db = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/db/kraken2", checkIfExists: true) ]
db = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
KRAKEN2_RUN ( input, db )
}
workflow test_kraken2_run_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
db = [ file("${launchDir}/tests/data/genomics/sarscov2/genome/db/kraken2", checkIfExists: true) ]
db = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
KRAKEN2_RUN ( input, db )
}

2
tests/software/kraken2/run/test.yml
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@ -28,4 +28,4 @@
- path: output/kraken2/test.unclassified_2.fastq.gz
should_exist: true
- path: output/kraken2/test.kraken2.report.txt
md5sum: 5fb165fd0bdf920ff6cf6f734371a4cf
md5sum: 4227755fe40478b8d7dc8634b489761e

2
tests/software/untar/main.nf
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@ -5,7 +5,7 @@ nextflow.enable.dsl = 2
include { UNTAR } from '../../../software/untar/main.nf' addParams( options: [:] )
workflow test_untar {
input = file("${launchDir}/tests/data/generic/test.txt.tar.gz", checkIfExists: true)
input = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
UNTAR ( input )
}

8
tests/software/untar/test.yml
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@ -3,5 +3,9 @@
tags:
- untar
files:
- path: output/untar/test.txt
md5sum: 7171d4ec2ad0882fab4b0142536d93a1
- path: output/untar/kraken2/hash.k2d
md5sum: 8b8598468f54a7087c203ad0190555d9
- path: output/untar/kraken2/opts.k2d
md5sum: a033d00cf6759407010b21700938f543
- path: output/untar/kraken2/taxo.k2d
md5sum: 094d5891cdccf2f1468088855c214b2c