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Merge pull request #381 from nf-core/fix/samplename-join
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Fix/samplename join
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@edmundmiller
edmundmiller authored Feb 23, 2024
2 parents b9ca80e + 457f9d6 commit 1faa12b
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Showing 7 changed files with 577 additions and 199 deletions.
168 changes: 125 additions & 43 deletions tests/pipeline/bismark/main.nf.test
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258 changes: 194 additions & 64 deletions tests/pipeline/bismark/main.nf.test.snap
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78 changes: 57 additions & 21 deletions tests/pipeline/bismark_hisat/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -19,33 +19,52 @@ nextflow_pipeline {
assertAll(
{ assert workflow.success },
{ assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam"),
path("$outputDir/bismark_hisat/deduplicated/SRR389222_trimmed_bismark_hisat2.deduplicated.bam"),
path("$outputDir/bismark_hisat/deduplicated/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bam"),
path("$outputDir/bismark_hisat/deduplicated/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bam"),
path("$outputDir/bismark_hisat/deduplicated/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bam"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"),
path("$outputDir/cat/SRR389222.merged.fastq.gz"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"),
path("$outputDir/qualimap/Ecoli/genome_results.txt"),
path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") },
path("$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 snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_1_val_1_bismark_hisat2_PE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_trimmed_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub1_trimmed_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/Ecoli_1_val_1_bismark_hisat2_PE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_trimmed_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub1_trimmed_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_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/bismark_hisat/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("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() }
{ assert new File("$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() }
)
}
}
Expand Down Expand Up @@ -82,29 +101,46 @@ nextflow_pipeline {
assertAll(
{ assert workflow.success },
{ assert snapshot(path("$outputDir/bismark_hisat/alignments/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam"),
path("$outputDir/bismark_hisat/alignments/SRR389222.merged_bismark_hisat2.bam"),
path("$outputDir/bismark_hisat/alignments/SRR389222_sub1_bismark_hisat2.bam"),
path("$outputDir/bismark_hisat/alignments/SRR389222_sub2_bismark_hisat2.bam"),
path("$outputDir/bismark_hisat/alignments/SRR389222_sub3_bismark_hisat2.bam"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222.merged_bismark_hisat2.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub1_bismark_hisat2.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub2_bismark_hisat2.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub3_bismark_hisat2.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222.merged_bismark_hisat2.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub1_bismark_hisat2.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub2_bismark_hisat2.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub3_bismark_hisat2.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222.merged_bismark_hisat2.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub1_bismark_hisat2.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub2_bismark_hisat2.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub3_bismark_hisat2.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222.merged_bismark_hisat2_splitting_report.txt"),
path("$outputDir/cat/SRR389222.merged.fastq.gz"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub1_bismark_hisat2_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub2_bismark_hisat2_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub3_bismark_hisat2_splitting_report.txt"),
path("$outputDir/qualimap/Ecoli/genome_results.txt"),
path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") },
path("$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_rrbs") },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222.merged_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub1_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub2_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub3_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222.merged_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub1_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub2_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub3_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_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/bismark_hisat/multiqc_report.html").exists() }
)
}
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