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test(#392): Add boilerplate for tests #393

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merged 7 commits into from
May 17, 2024
Merged

test(#392): Add boilerplate for tests #393

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30c76b5
test(#392): Add boilerplate for tests
edmundmiller Mar 29, 2024
825d441
Update samplesheet.csv
FelixKrueger Mar 30, 2024
86b4f7b
Update samplesheet.csv
FelixKrueger Apr 4, 2024
880e473
fix paths
maxulysse Apr 4, 2024
94a3856
fix: fix path to script
maxulysse Apr 4, 2024
d1c5d0e
Merge branch 'dev' into fix/tech-reps
maxulysse May 17, 2024
f36cbdf
add very simple tests
maxulysse May 17, 2024
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10 changes: 10 additions & 0 deletions tests/pipeline/bismark/assets/samplesheet.csv
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sample,fastq_1,fastq_2,genome
SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
SRR389222_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
SRR389222_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
SRR389222_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,
Ecoli_uniq1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
Ecoli_uniq2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
Ecoli_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
Ecoli_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,
70 changes: 70 additions & 0 deletions tests/pipeline/bismark/samplesheet.nf.test
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nextflow_pipeline {

name "Test Replicate Handling"
script "main.nf"

tag "pipeline"


test("Should ____") {
when {
params {
input = "$baseDir/tests/pipeline/bismark/assets/samplesheet.csv"
outdir = "$outputDir"
}
}

then {
assertAll(
{ assert workflow.success },
// TODO Output names should be as expected
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
{ assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"),
path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"),
path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat"),
path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.stats"),
path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat"),
path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.stats"),
path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat"),
path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.stats"),
path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam"),
path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam.bai"),
path("$outputDir/bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam"),
path("$outputDir/bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai"),
path("$outputDir/bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam"),
path("$outputDir/bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai"),
path("$outputDir/bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam"),
path("$outputDir/bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai"),
path("$outputDir/bwameth/reference_genome/").list(),
path("$outputDir/methyldackel/Ecoli.markdup.sorted_CpG.bedGraph"),
path("$outputDir/methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph"),
path("$outputDir/methyldackel/SRR389222_sub2.markdup.sorted_CpG.bedGraph"),
path("$outputDir/methyldackel/SRR389222_sub3.markdup.sorted_CpG.bedGraph"),
path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"),
path("$outputDir/methyldackel/mbias/SRR389222_sub1.mbias.txt"),
path("$outputDir/methyldackel/mbias/SRR389222_sub2.mbias.txt"),
path("$outputDir/methyldackel/mbias/SRR389222_sub3.mbias.txt"),
path("$outputDir/qualimap/Ecoli/genome_results.txt"),
path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"),
path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"),
path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end") },
{ assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() },
{ assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() },
{ assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli.markdup.sorted.MarkDuplicates.metrics.txt").exists() },
{ assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt").exists() },
{ assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.MarkDuplicates.metrics.txt").exists() },
{ assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.MarkDuplicates.metrics.txt").exists() }
)
}
}

}
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