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nf-core_modules/tests/config/test_data.config

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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
2021-03-24 18:28:07 +00:00
// 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 = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"
update tests for new config (#384) * update tests for new config * fix quast, update more * more updates! * more tests updated * fix tests, added tabix gff3.gz * Delete main.nf Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 19:22:06 +00:00
genome_gff3_gz = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3.gz"
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
2021-03-24 18:28:07 +00:00
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 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
PR for sequenzautils/bam2seqz (#395) * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 05:08:27 +00:00
test_wig_gz = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
adding fasttree module (#412) * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * remove TODO * update test data naming * further test data naming updates * remove options in favour of $options.args * ensure non standard exit codes don't cause an issue * update md5sum
2021-04-08 17:15:23 +00:00
all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
contigs_fasta = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta"
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
2021-03-24 18:28:07 +00:00
}
'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 = "${test_data_dir}/genomics/sarscov2/nanopore/fastq/test.fastq.gz"
Nanoplot and sequencing_summary.txt for Nanopore test data (#364) * add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output
2021-04-09 07:31:38 +00:00
test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
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
2021-03-24 18:28:07 +00:00
}
}
'homo_sapiens' {
'illumina' {
test_paired_end_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test_paired_end.bam"
}
}
}
PR for sequenzautils/bam2seqz (#395) * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 05:08:27 +00:00
}
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