diff --git a/tests/bismark_emseq_clip_r1.nf.test b/tests/bismark_emseq_clip_r1.nf.test index 8773e234..2b13d73e 100644 --- a/tests/bismark_emseq_clip_r1.nf.test +++ b/tests/bismark_emseq_clip_r1.nf.test @@ -14,64 +14,29 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - path("$outputDir/bismark/deduplicated/Ecoli.deduplicated.sorted.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.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("Bismark em_seq_clip_r1") }, + // Number of tasks + workflow.trace.tasks().size(), - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/Ecoli_1_val_1_bismark_bt2_pe.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/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("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/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("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() }, + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + // All stable path name + stable_name*.name, + + // All files with stable contents + stable_path + ).match() } ) + } } diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index d0853219..cfdc7583 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -1,6 +1,7 @@ { - "software_versions": { + "Bismark em_seq_clip_r1": { "content": [ + 47, { "BISMARK_ALIGN": { "bismark": "0.24.0" @@ -21,33 +22,473 @@ "Workflow": { "nf-core/methylseq": "v2.7.0dev" } - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-21T15:15:17.855300333" - }, - "Bismark em_seq_clip_r1": { - "content": [ - "Ecoli.deduplicated.sorted.bam:md5,e021d31b331c251551b88f3bde6c21d8", - "SRR389222_sub1.deduplicated.sorted.bam:md5,d4b7d1d435f6eaf22940e83b4c7d694a", - "SRR389222_sub2.deduplicated.sorted.bam:md5,05f7fe5fcb322443cfe2087c5e948df8", - "SRR389222_sub3.deduplicated.sorted.bam:md5,3fddd164b18ab9da8ec2a21813587042", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,f662ef520f5e483cd6f2a4925afe2283", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,330d25130120699a9ca4cf7152f9ac18", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,9cd7348188fb06c7648b1453db5270c9", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,aab193316d15edf54271f7d3270ae963", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,81a0d0749e3df600572188afec21a9e3", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,818aaadc83209032dc234717455ae91d", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,51f024d22277e740f07b6fca27b2b159", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,beb2a4e9ef24ad73aa6807ddd17899d7", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,167ae8eabdeb46a3322f549f3b7c1285", + }, [ + "bismark", + "alignments", + "logs", + "Ecoli_1_val_1_bismark_bt2_PE_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "deduplicated", + "Ecoli.deduplicated.sorted.bam", + "Ecoli.deduplicated.sorted.bam.bai", + "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.deduplicated.sorted.bam.bai", + "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.deduplicated.sorted.bam.bai", + "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.deduplicated.sorted.bam.bai", + "logs", + "Ecoli_1_val_1_bismark_bt2_pe.deduplication_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt", + "methylation_calls", + "bedGraph", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "mbias", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "methylation_calls", + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "methylation_coverage", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "splitting_report", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "reports", + "Ecoli_1_val_1_bismark_bt2_PE_report.html", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.html", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.html", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.html", + "summary", + "bismark_summary_report.html", + "bismark_summary_report.txt", + "fastqc", + "Ecoli_1_fastqc.html", + "Ecoli_2_fastqc.html", + "SRR389222_sub1_fastqc.html", + "SRR389222_sub2_fastqc.html", + "SRR389222_sub3_fastqc.html", + "zips", + "Ecoli_1_fastqc.zip", + "Ecoli_2_fastqc.zip", + "SRR389222_sub1_fastqc.zip", + "SRR389222_sub2_fastqc.zip", + "SRR389222_sub3_fastqc.zip", + "multiqc", + "bismark", + "multiqc_data", + "bismark-methylation-dp.txt", + "bismark_alignment.txt", + "bismark_deduplication.txt", + "bismark_mbias_CHG_R1.txt", + "bismark_mbias_CHG_R2.txt", + "bismark_mbias_CHH_R1.txt", + "bismark_mbias_CHH_R2.txt", + "bismark_mbias_CpG_R1.txt", + "bismark_mbias_CpG_R2.txt", + "bismark_strand_alignment.txt", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "multiqc.log", + "multiqc_bismark_alignment.txt", + "multiqc_bismark_dedup.txt", + "multiqc_bismark_methextract.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_qualimap_bamqc_genome_results.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "qualimap_coverage_histogram.txt", + "qualimap_gc_content.txt", + "qualimap_genome_fraction.txt", + "qualimap_insert_size.txt", + "multiqc_plots", + "pdf", + "bismark-methylation-dp.pdf", + "bismark_alignment-cnt.pdf", + "bismark_alignment-pct.pdf", + "bismark_deduplication-cnt.pdf", + "bismark_deduplication-pct.pdf", + "bismark_mbias_CHG_R1.pdf", + "bismark_mbias_CHG_R2.pdf", + "bismark_mbias_CHH_R1.pdf", + "bismark_mbias_CHH_R2.pdf", + "bismark_mbias_CpG_R1.pdf", + "bismark_mbias_CpG_R2.pdf", + "bismark_strand_alignment-cnt.pdf", + "bismark_strand_alignment-pct.pdf", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_adapter_content_plot.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "general_stats_table.pdf", + "qualimap_coverage_histogram.pdf", + "qualimap_gc_content.pdf", + "qualimap_genome_fraction.pdf", + "qualimap_insert_size.pdf", + "png", + "bismark-methylation-dp.png", + "bismark_alignment-cnt.png", + "bismark_alignment-pct.png", + "bismark_deduplication-cnt.png", + "bismark_deduplication-pct.png", + "bismark_mbias_CHG_R1.png", + "bismark_mbias_CHG_R2.png", + "bismark_mbias_CHH_R1.png", + "bismark_mbias_CHH_R2.png", + "bismark_mbias_CpG_R1.png", + "bismark_mbias_CpG_R2.png", + "bismark_strand_alignment-cnt.png", + "bismark_strand_alignment-pct.png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "fastqc-status-check-heatmap.png", + "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_top_overrepresented_sequences_table.png", + "general_stats_table.png", + "qualimap_coverage_histogram.png", + "qualimap_gc_content.png", + "qualimap_genome_fraction.png", + "qualimap_insert_size.png", + "svg", + "bismark-methylation-dp.svg", + "bismark_alignment-cnt.svg", + "bismark_alignment-pct.svg", + "bismark_deduplication-cnt.svg", + "bismark_deduplication-pct.svg", + "bismark_mbias_CHG_R1.svg", + "bismark_mbias_CHG_R2.svg", + "bismark_mbias_CHH_R1.svg", + "bismark_mbias_CHH_R2.svg", + "bismark_mbias_CpG_R1.svg", + "bismark_mbias_CpG_R2.svg", + "bismark_strand_alignment-cnt.svg", + "bismark_strand_alignment-pct.svg", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.svg", + 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"coverage_histogram.txt:md5,be94408b8524e6bd1ae31865d0d09f4c", + "duplication_rate_histogram.txt:md5,6309eddf20ae50627a22ab2c722e5b2d", + "genome_fraction_coverage.txt:md5,d84f3c4eb9bab78a0505ff3846e14a4d", + "mapped_reads_gc-content_distribution.txt:md5,929110dec78f0b75a81b8de6dec41acb", + "mapped_reads_nucleotide_content.txt:md5,96ce928c723c792df54856458fbd2bff", + "mapping_quality_across_reference.txt:md5,c1ef6aa70a21fd9dd78ae011c57edfaf", + "mapping_quality_histogram.txt:md5,540af5818b5c171ed7c7d4ff70688fa0", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + 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"genome_uniq_read_starts_histogram.png:md5,306621e1226cd587fdeafd9b622e2982", + "coverage_across_reference.txt:md5,5f6ec1e01178bc0124de83e40f6be40f", + "coverage_histogram.txt:md5,bf5bc5ad630c0277561270eb8c08ebfa", + "duplication_rate_histogram.txt:md5,c9c9039749f9bae1241614c0b4553429", + "genome_fraction_coverage.txt:md5,f5ef37075d8c9ae53782c3341c473df1", + "mapped_reads_gc-content_distribution.txt:md5,6c5ab32c61ae3da1662476075d6e5a9a", + "mapped_reads_nucleotide_content.txt:md5,64fc44b6c7b837eb7565b5366275e96e", + "mapping_quality_across_reference.txt:md5,27ddade530da51346a0917dde0b0e816", + "mapping_quality_histogram.txt:md5,570c897efc7bcb475d3f98b053fd1db1", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + 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"genome_mapping_quality_histogram.png:md5,62e2d6836200c9b14a57577e6ca09240", + "genome_reads_content_per_read_position.png:md5,67448e3658e7e05029ac92b6e141d56a", + "genome_uniq_read_starts_histogram.png:md5,a374363dff1ba243998f78301b3e408b", + "coverage_across_reference.txt:md5,04f145cfd64ac9201c3aec079b3d3b15", + "coverage_histogram.txt:md5,e56d4fa32ff3a3b353e85ade466d4d05", + "duplication_rate_histogram.txt:md5,5ba94ffcc34de2e00001260557f0e414", + "genome_fraction_coverage.txt:md5,f52c58853afd8a6cb407bd4277cf530e", + "mapped_reads_gc-content_distribution.txt:md5,ebdf1092102ff3e06a965b53b7f1fc4d", + "mapped_reads_nucleotide_content.txt:md5,b8f95fd9ce7d994d7af033c62f7b45e8", + "mapping_quality_across_reference.txt:md5,27ddade530da51346a0917dde0b0e816", + "mapping_quality_histogram.txt:md5,1d5d75ee7b68752b12a2e6d6d3042ea9" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-21T15:15:17.615342035" + "timestamp": "2024-09-22T12:22:53.256606954" } } \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test b/tests/bismark_nomeseq.nf.test index 50f3b083..8e265315 100644 --- a/tests/bismark_nomeseq.nf.test +++ b/tests/bismark_nomeseq.nf.test @@ -13,66 +13,29 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub1.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub1.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/deduplicated/Ecoli.deduplicated.sorted.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.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("Bismark_nomeseq") }, + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.tasks().size(), - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/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("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/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("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() }, + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_nomeseq_software_versions") }, + // All stable path name + stable_name*.name, + + // All files with stable contents + stable_path + ).match() } ) + } } diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index 54317180..42f27481 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -1,31 +1,540 @@ { - "Bismark_nomeseq": { + "Bismark nomeseq": { "content": [ - "Ecoli.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", - "Ecoli.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", - "SRR389222_sub1.NOMe.CpG.cov.gz:md5,087f5da64b9ab087a0e22fa11536871e", - "SRR389222_sub2.NOMe.CpG.cov.gz:md5,016eabe6c88ef719d8edffbe13d1b2ce", - "SRR389222_sub3.NOMe.CpG.cov.gz:md5,85098361910f7398528dcbb0e46a7561", - "SRR389222_sub1.NOMe.GpC.cov.gz:md5,25211d7e44488baf6193f753a5095b2f", - "SRR389222_sub2.NOMe.GpC.cov.gz:md5,10837f6099f63dc4aae2895d821a582e", - "SRR389222_sub3.NOMe.GpC.cov.gz:md5,8005a9dad4d0f5562a3c7cf215a18908", - "Ecoli.deduplicated.sorted.bam:md5,8aa7a2125d9a57dc377fc4e01581762f", - "SRR389222_sub1.deduplicated.sorted.bam:md5,63986824e4dceb3742b6ae03e9094e1e", - "SRR389222_sub2.deduplicated.sorted.bam:md5,7c54ceae346daf62a1e9d850577a44fe", - 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"duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1", + "genome_fraction_coverage.txt:md5,72555b3e32396cb9df359c10d6db0e8d", + "mapped_reads_gc-content_distribution.txt:md5,66c54a24d30784028de35fe4b0c35ce3", + "mapped_reads_nucleotide_content.txt:md5,2a2d04e030d228b9e6c3267e6f9e6225", + "mapping_quality_across_reference.txt:md5,33942e63dd23b4c0e307cd2f8c2fb299", + "mapping_quality_histogram.txt:md5,5d14a661b9d3d59e4dfcb841084a6def", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", + "genome_coverage_0to50_histogram.png:md5,dd2484bbca9a7c6f55def856746afa46", + "genome_coverage_across_reference.png:md5,f8b9f96f7e9de8d870e489f347272252", + "genome_coverage_histogram.png:md5,4c077ab4bc677b24650397f4c697b59c", + "genome_coverage_quotes.png:md5,8860c47649c597df8271868122cf167d", + "genome_gc_content_per_window.png:md5,5ea2ba99c19eaaa24140dc41f30fd427", + "genome_mapping_quality_across_reference.png:md5,60413ab77c118c3242f8cb1c6b5a0f35", + "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956", + "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157", + "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19", + "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2", + "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80", + "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8", + "genome_fraction_coverage.txt:md5,ca40e719b074696357494e3cba520d4a", + "mapped_reads_gc-content_distribution.txt:md5,4927664b2fcd95fe01daeb1315fffdf7", + "mapped_reads_nucleotide_content.txt:md5,ffdced213cd2a96408c4b9794092bd80", + "mapping_quality_across_reference.txt:md5,a15709e1860fdd7deaf86dfa0d461144", + "mapping_quality_histogram.txt:md5,feafb188d85e486d16374117565d88d1", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a", + "genome_coverage_0to50_histogram.png:md5,2cfd88b3aa6b417f73c0fc39f1a6f633", + "genome_coverage_across_reference.png:md5,7ee66fcdc90f02a84ae95e4a4ac8c7c3", + "genome_coverage_histogram.png:md5,c4caed1ef14844f6da4cc7b92543b379", + "genome_coverage_quotes.png:md5,66d0e8e1c0885b5f8ccf4683ebadbcd8", + "genome_gc_content_per_window.png:md5,2112a5d7c78711258303ef6fdc088346", + "genome_mapping_quality_across_reference.png:md5,2a066966adca0027fce00dbabf12f4b1", + "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92", + "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de", + "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03", + "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce", + "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301", + "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b", + "genome_fraction_coverage.txt:md5,48f654e7179fdb7c4830ceb8f862af0b", + "mapped_reads_gc-content_distribution.txt:md5,a603a3d326e811f38f448cd3d017b4a8", + "mapped_reads_nucleotide_content.txt:md5,783a0fb23148a56c1c78a21d774109eb", + "mapping_quality_across_reference.txt:md5,d9bafb5cc106bbd1dc7e31439c618f19", + "mapping_quality_histogram.txt:md5,560e85b88f5f90e9ad7ad93ffef42d6f" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-21T14:44:33.711085245" + "timestamp": "2024-09-22T12:17:50.582474447" } } \ No newline at end of file diff --git a/tests/bismark_rrbs.nf.test b/tests/bismark_rrbs.nf.test index 955721ff..86225681 100644 --- a/tests/bismark_rrbs.nf.test +++ b/tests/bismark_rrbs.nf.test @@ -13,53 +13,29 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/alignments/Ecoli_1_val_1_bismark_bt2_pe.bam"), - path("$outputDir/bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam"), - path("$outputDir/bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam"), - path("$outputDir/bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2_splitting_report.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("Bismark_rrbs") }, + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.tasks().size(), - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/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("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + // All stable path name + stable_name*.name, + + // All files with stable contents + stable_path + ).match() } ) + } } diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index db991d35..d03cacba 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -1,6 +1,7 @@ { - "software_versions": { + "Bismark rrbs": { "content": [ + 43, { "BISMARK_ALIGN": { "bismark": "0.24.0" @@ -21,33 +22,468 @@ "Workflow": { "nf-core/methylseq": "v2.7.0dev" } - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-21T14:47:15.973248888" - }, - "Bismark_rrbs": { - "content": [ - "Ecoli_1_val_1_bismark_bt2_pe.bam:md5,8b3001c60505c1ed07dcca3e7b07ce8f", - "SRR389222_sub1_trimmed_bismark_bt2.bam:md5,b8ab3a6b07c4a319f051630bd9d3c8fe", - "SRR389222_sub2_trimmed_bismark_bt2.bam:md5,3d2aa63597258e8136387a421bba8d3e", - "SRR389222_sub3_trimmed_bismark_bt2.bam:md5,c5ac3876f32889dc22850ecce137c58f", - "Ecoli_1_val_1_bismark_bt2_pe.bedGraph.gz:md5,2691bc94521625f665ea62b357022e4e", - "SRR389222_sub1_trimmed_bismark_bt2.bedGraph.gz:md5,19b360cef6da9e51a9aed103bdc20c59", - "SRR389222_sub2_trimmed_bismark_bt2.bedGraph.gz:md5,e3391beb85c4718b897850bd0b724238", - "SRR389222_sub3_trimmed_bismark_bt2.bedGraph.gz:md5,77237eb7bd3b1d213798ea69c9bd1dc0", - "Ecoli_1_val_1_bismark_bt2_pe.M-bias.txt:md5,198181d02bd7f42f9c7762b383d6f9f5", - "SRR389222_sub1_trimmed_bismark_bt2.M-bias.txt:md5,85e560f0b24650662740311e7e0e68c5", - "SRR389222_sub2_trimmed_bismark_bt2.M-bias.txt:md5,1dbb052bca91de848e3136397904de5b", - "SRR389222_sub3_trimmed_bismark_bt2.M-bias.txt:md5,75f664cedec907f51bc52ac1fca0d178", - "Ecoli_1_val_1_bismark_bt2_pe.bismark.cov.gz:md5,60eac8132590c72d1606d41eb4adcb30", - "SRR389222_sub1_trimmed_bismark_bt2.bismark.cov.gz:md5,7660c828d0ea61dee7dfe01dd8330461", - "SRR389222_sub2_trimmed_bismark_bt2.bismark.cov.gz:md5,fd27bbf4f8e0ab429066c8b0bb70279d", - "SRR389222_sub3_trimmed_bismark_bt2.bismark.cov.gz:md5,d3c196f28a99b8c28da654f8d9a23666", + }, + [ + "bismark", + "alignments", + "Ecoli_1_val_1_bismark_bt2_pe.bam", + "SRR389222_sub1_trimmed_bismark_bt2.bam", + "SRR389222_sub2_trimmed_bismark_bt2.bam", + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "logs", + "Ecoli_1_val_1_bismark_bt2_PE_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "deduplicated", + "Ecoli.deduplicated.sorted.bam", + "Ecoli.deduplicated.sorted.bam.bai", + "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.deduplicated.sorted.bam.bai", + "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.deduplicated.sorted.bam.bai", + "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.deduplicated.sorted.bam.bai", + "methylation_calls", + "bedGraph", + "Ecoli_1_val_1_bismark_bt2_pe.bedGraph.gz", + "SRR389222_sub1_trimmed_bismark_bt2.bedGraph.gz", + "SRR389222_sub2_trimmed_bismark_bt2.bedGraph.gz", + "SRR389222_sub3_trimmed_bismark_bt2.bedGraph.gz", + "mbias", + "Ecoli_1_val_1_bismark_bt2_pe.M-bias.txt", + "SRR389222_sub1_trimmed_bismark_bt2.M-bias.txt", + "SRR389222_sub2_trimmed_bismark_bt2.M-bias.txt", + "SRR389222_sub3_trimmed_bismark_bt2.M-bias.txt", + "methylation_calls", + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.txt.gz", + "CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.txt.gz", + "CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.txt.gz", + "CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.txt.gz", + 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"fastqc_overrepresented_sequences_plot.txt:md5,7402f1164f8aa05406703fb0c18b4428", + "fastqc_per_base_n_content_plot.txt:md5,d852ed1029342edc9981ad3105abaedb", + "fastqc_per_base_sequence_quality_plot.txt:md5,1e9c4701fdb3367be21980455010010a", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,af5e3874769dcda665730aaef2b76e9e", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,7b21b780b32694e8a4107285f5037e42", + "fastqc_per_sequence_quality_scores_plot.txt:md5,d41664b3ad203d095aee006588c93298", + "fastqc_sequence_counts_plot.txt:md5,47e0b371031eb1fad2cd6be86206265b", + "fastqc_sequence_duplication_levels_plot.txt:md5,00b66074303680ddba5a5f7dd9ab71cc", + "multiqc_bismark_alignment.txt:md5,248fdb22ebe3be492c8c523631e32635", + "multiqc_bismark_methextract.txt:md5,b0265cff53ccc91da528d458a3a8ddc8", + "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", + "multiqc_cutadapt.txt:md5,75a6c55468d07b9391a2f2f4ceeabd3e", + "multiqc_qualimap_bamqc_genome_results.txt:md5,df70c80d68701f6f3782318d2d1f6749", + "multiqc_software_versions.txt:md5,514aa3d6efcd5828b1e5e85b5c82f198", + "qualimap_coverage_histogram.txt:md5,270ed514982e0f986c484227eab03a16", + "qualimap_gc_content.txt:md5,df3d10836c4e0e11f6355a9e637f5985", + "qualimap_genome_fraction.txt:md5,2811e281f58d35fcde29054f7001c54a", + "qualimap_insert_size.txt:md5,f4304b6cd88219729b621fbbbcb88b78", + "bismark_alignment-cnt.png:md5,f309172c64aa869d9309868a872e839d", + "bismark_alignment-pct.png:md5,539763d8bcd84ac19895fed4b60bd399", + "bismark_mbias_CHG_R1.png:md5,50ba16cc5951dd8ef632d9d09bdc16b6", + "bismark_mbias_CHG_R2.png:md5,e7c0ed3d988c6562443ebbf27f072efe", + "bismark_mbias_CHH_R1.png:md5,a2faa6ec03c8207db831a17acb749dff", + "bismark_mbias_CHH_R2.png:md5,a7f1994cefa45554f6100992629e146d", + "bismark_mbias_CpG_R1.png:md5,3ac8c896f0082aad8944e28fa011d33e", + "bismark_mbias_CpG_R2.png:md5,c04f1ef61153b8831abcf7cf016f3f61", + 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"genome_reads_content_per_read_position.png:md5,65b2642bbbeafd082f78df575384c7b4", + "genome_uniq_read_starts_histogram.png:md5,9b9cc4b450beec5c254482822d3b75eb", + "coverage_across_reference.txt:md5,0412f5393c2d6c38e24b298a29207832", + "coverage_histogram.txt:md5,c66a1041626dd043ee8900f0568f96c5", + "duplication_rate_histogram.txt:md5,4a9f605621f1ad7c0e4b816042541efc", + "genome_fraction_coverage.txt:md5,c75063a6bc66540f2a77e13d3c3cc858", + "insert_size_across_reference.txt:md5,eee57ae9151b395a40ec93ab47d5f52f", + "insert_size_histogram.txt:md5,e9f571e90fa7892568462abe5aed45e1", + "mapped_reads_gc-content_distribution.txt:md5,d95d5dba619621907d99c3fe85324774", + "mapped_reads_nucleotide_content.txt:md5,ddfa5b9cb8d5d14940e826ea7e8e25a0", + "mapping_quality_across_reference.txt:md5,51bc42b3c28e9bc2a648b595dd0a16ad", + "mapping_quality_histogram.txt:md5,dd994cf923082ba126df697357cce658", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + 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"genome_coverage_quotes.png:md5,016458abce14522131eb198f9a3942d6", + "genome_gc_content_per_window.png:md5,3a9d4612604f3d8fd91685ba04386a6b", + "genome_mapping_quality_across_reference.png:md5,7a218a7f069ebdc296d2b50a28429127", + "genome_mapping_quality_histogram.png:md5,21771951430da26aa1de65b1058ca917", + "genome_reads_content_per_read_position.png:md5,9a870d3eab467880828674617491bf32", + "genome_uniq_read_starts_histogram.png:md5,11584f87d14ecc58c56852088184a8f6", + "coverage_across_reference.txt:md5,19ec1fcc21c51552e09958af3b19a368", + "coverage_histogram.txt:md5,219cfb1206b780f0c39c6dd5a9c1d7bc", + "duplication_rate_histogram.txt:md5,26627aec41f7da64bc58f3e5c493167f", + "genome_fraction_coverage.txt:md5,f1da27b3770f169979fa503ad9fc9844", + "mapped_reads_gc-content_distribution.txt:md5,516e9558539bab79678e99542a63dca4", + "mapped_reads_nucleotide_content.txt:md5,9183ff401297005956c5cbae3e4e3d58", + "mapping_quality_across_reference.txt:md5,65d4d8dcbc4cbe58b32979ed1da3e982", + "mapping_quality_histogram.txt:md5,ee6974502e2b91140f75ea9b61ce1e41", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "genome_results.txt:md5,eccab1342de8fbbf5e5e547cd861b704", + "genome_coverage_0to50_histogram.png:md5,a35720863d88e9d64d4cc331dd664054", + "genome_coverage_across_reference.png:md5,e1f222bfd6227026b0f1406f08d95f6e", + "genome_coverage_histogram.png:md5,dfc6a499621d0ac2df7cdd890c1195e7", + "genome_coverage_quotes.png:md5,a388a782f95760ccecec6cd62a0ed03a", + "genome_gc_content_per_window.png:md5,cb2fa3cdd99f590a963c46463adc0bf6", + "genome_mapping_quality_across_reference.png:md5,337fe133d009b7336dcf8f514271b2e7", + "genome_mapping_quality_histogram.png:md5,7f559b8f2647234dfa4852644f11271f", + "genome_reads_content_per_read_position.png:md5,3fe1d60a39ccf297dfc1753552a1200a", + "genome_uniq_read_starts_histogram.png:md5,275e9c6dc8b05fa96d779cd159f94bbf", + "coverage_across_reference.txt:md5,dff746a8a42363f6a63d31dc388db054", + "coverage_histogram.txt:md5,24b19558a8ed50fb82f0cca85576e6c7", + "duplication_rate_histogram.txt:md5,5a9893b6051ac725ff0858f03b8c1d9e", + "genome_fraction_coverage.txt:md5,7bb31fa0f86783b72de81862130b0dd2", + "mapped_reads_gc-content_distribution.txt:md5,a844e905bb35783c1cc9a5012a4c1b4f", + "mapped_reads_nucleotide_content.txt:md5,9f2238cefca7d4d396166493531b023d", + "mapping_quality_across_reference.txt:md5,09972dd7e688343c0d8d4e1cfa0f0ed3", + "mapping_quality_histogram.txt:md5,f4558df0222e1480a46b5c4fc31ca5f5", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "genome_results.txt:md5,8b11703c6ee4e2a73d7d2624bda6b6ba", + "genome_coverage_0to50_histogram.png:md5,e7461ecc40075b1053e85bb19133e5ec", + "genome_coverage_across_reference.png:md5,fb94c353d5f4c82529e502942bd62532", + "genome_coverage_histogram.png:md5,08187a1c49e4649b1947185f5713ea48", + "genome_coverage_quotes.png:md5,283c7c1318b29cd1dc85572d5226bcf2", + "genome_gc_content_per_window.png:md5,95a7825de361abfadcb635acf1fe5942", + "genome_mapping_quality_across_reference.png:md5,af48967bec418f07cf8261dedc7a9d04", + "genome_mapping_quality_histogram.png:md5,a130758df8b6d7557c10702a6ff0d03f", + "genome_reads_content_per_read_position.png:md5,9114c974715722d293a19c42059b480e", + "genome_uniq_read_starts_histogram.png:md5,5da3aadb7b5f8efe259e10719f2e16f5", + "coverage_across_reference.txt:md5,aa07899188f5bbf958eee91c60dc7e9a", + "coverage_histogram.txt:md5,3045dc5ebbaf79241cac050999c18d0f", + "duplication_rate_histogram.txt:md5,4fe6535303d5079153f465183fc7ef48", + "genome_fraction_coverage.txt:md5,bc79d169a3b0d1cd2806e64cb453c8f0", + "mapped_reads_gc-content_distribution.txt:md5,90cdf405f32b2e4ac7df8f4e69fded27", + "mapped_reads_nucleotide_content.txt:md5,11e8cff660b0ecec303ff425951badd2", + "mapping_quality_across_reference.txt:md5,eeea15df6a449af86a1c59a3e8859a91", + "mapping_quality_histogram.txt:md5,ba639bdc782f882ce55fcd81d1217fd3" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-21T14:47:13.985902685" + "timestamp": "2024-09-22T12:11:20.133439826" } } \ No newline at end of file diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test b/tests/bismark_save_reference_save_align_intermeds.nf.test index 4b4d77c8..6e81aacb 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test @@ -15,78 +15,29 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - bam("$outputDir/bismark/alignments/Ecoli_1_val_1_bismark_bt2_pe.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/Ecoli.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/SRR389222_sub1.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/SRR389222_sub2.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/SRR389222_sub3.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/Ecoli.deduplicated.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam").getReadsMD5(), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt") - ).match("save_reference-save_align_intermeds") }, + // Number of tasks + workflow.trace.tasks().size(), - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/Ecoli_1_val_1_bismark_bt2_pe.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_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("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/Ecoli_1_val_1_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/Ecoli_2_val_2_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/SRR389222_sub1_trimmed_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/SRR389222_sub2_trimmed_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/SRR389222_sub3_trimmed_fastqc.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("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() }, + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + // All stable path name + stable_name*.name, + + // All files with stable contents + stable_path + ).match() } ) + } } diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap index c908e133..e2b4a1a9 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -1,6 +1,7 @@ { - "software_versions": { + "Bismark save_reference-save_align_intermeds": { "content": [ + 47, { "BISMARK_ALIGN": { "bismark": "0.24.0" @@ -21,37 +22,511 @@ "Workflow": { "nf-core/methylseq": "v2.7.0dev" } - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-21T12:52:22.52362649" - }, - "save_reference-save_align_intermeds": { - "content": [ - "fad4414ebdaafdb15e0584b393400b27", - "a54ab7c96f9523a4ccd25fd69f6905f8", - "fa0f34c0d0d4d321b89973f23e033aa1", - "934288bfc59d40ff7e73706d07815fb", - "d347232a4fc5b1e02e98254b6ce97ae6", - "a94aeadc2acebd0a46647bb95acf2d55", - "29648af285a183ae2194790b5a325186", - "6579ca7e49b9d7760ea5b3f3456739a1", - "a54ab7c96f9523a4ccd25fd69f6905f8", - "3f11ef5fbbda3797fd6217728e4f00d3", - "b01f29fc1d8d46922a69df09c636b4c4", - "347195c04c9ffd2a2b10967a6682fc69", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,d31df76c1c9128299367ebfe740357b9", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,010f32001bbc7805f8e041f3ef0d9ea9", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,d42e09af121ae14f6e0de5779e317b0b", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,ed28b3cce432eecfae73bc4a071ec4ee", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b06ce0084e54193ff8c9b9dd0ec9757b", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b865b7fb6e1225feeb6aef3372ef0b1d", + }, [ + "bismark", + "alignments", + "Ecoli.sorted.bam", + "Ecoli_1_val_1_bismark_bt2_pe.bam", + "SRR389222_sub1.sorted.bam", + "SRR389222_sub1_trimmed_bismark_bt2.bam", + "SRR389222_sub2.sorted.bam", + "SRR389222_sub2_trimmed_bismark_bt2.bam", + "SRR389222_sub3.sorted.bam", + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "logs", + "Ecoli_1_val_1_bismark_bt2_PE_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "deduplicated", + "Ecoli.deduplicated.sorted.bam", + "Ecoli.deduplicated.sorted.bam.bai", + "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.deduplicated.sorted.bam.bai", + "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.deduplicated.sorted.bam.bai", + "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.deduplicated.sorted.bam.bai", + "logs", + "Ecoli_1_val_1_bismark_bt2_pe.deduplication_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt", + "methylation_calls", + "bedGraph", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "mbias", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "methylation_calls", + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "methylation_coverage", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "splitting_report", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "reference_genome", + "BismarkIndex", + "Bisulfite_Genome", + "CT_conversion", + "BS_CT.1.bt2", + "BS_CT.2.bt2", + "BS_CT.3.bt2", + "BS_CT.4.bt2", + "BS_CT.rev.1.bt2", + "BS_CT.rev.2.bt2", + "genome_mfa.CT_conversion.fa", + "GA_conversion", + "BS_GA.1.bt2", + "BS_GA.2.bt2", + "BS_GA.3.bt2", + "BS_GA.4.bt2", + "BS_GA.rev.1.bt2", + "BS_GA.rev.2.bt2", + "genome_mfa.GA_conversion.fa", + "genome.fa", + "reports", + "Ecoli_1_val_1_bismark_bt2_PE_report.html", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.html", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.html", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.html", + "summary", + "bismark_summary_report.html", + "bismark_summary_report.txt", + "fastqc", + "Ecoli_1_fastqc.html", + "Ecoli_2_fastqc.html", + "SRR389222_sub1_fastqc.html", + "SRR389222_sub2_fastqc.html", + "SRR389222_sub3_fastqc.html", + "zips", + "Ecoli_1_fastqc.zip", + "Ecoli_2_fastqc.zip", + "SRR389222_sub1_fastqc.zip", + "SRR389222_sub2_fastqc.zip", + "SRR389222_sub3_fastqc.zip", + "multiqc", + "bismark", + "multiqc_data", + "bismark-methylation-dp.txt", + "bismark_alignment.txt", + "bismark_deduplication.txt", + "bismark_mbias_CHG_R1.txt", + "bismark_mbias_CHG_R2.txt", + "bismark_mbias_CHH_R1.txt", + "bismark_mbias_CHH_R2.txt", + "bismark_mbias_CpG_R1.txt", + "bismark_mbias_CpG_R2.txt", + "bismark_strand_alignment.txt", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "multiqc.log", + "multiqc_bismark_alignment.txt", + "multiqc_bismark_dedup.txt", + "multiqc_bismark_methextract.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_qualimap_bamqc_genome_results.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "qualimap_coverage_histogram.txt", + "qualimap_gc_content.txt", + "qualimap_genome_fraction.txt", + "qualimap_insert_size.txt", + "multiqc_plots", + "pdf", + "bismark-methylation-dp.pdf", + "bismark_alignment-cnt.pdf", + "bismark_alignment-pct.pdf", + "bismark_deduplication-cnt.pdf", + "bismark_deduplication-pct.pdf", + "bismark_mbias_CHG_R1.pdf", + "bismark_mbias_CHG_R2.pdf", + "bismark_mbias_CHH_R1.pdf", + "bismark_mbias_CHH_R2.pdf", + "bismark_mbias_CpG_R1.pdf", + "bismark_mbias_CpG_R2.pdf", + "bismark_strand_alignment-cnt.pdf", + "bismark_strand_alignment-pct.pdf", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + 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"mapped_reads_gc-content_distribution.txt:md5,66c54a24d30784028de35fe4b0c35ce3", + "mapped_reads_nucleotide_content.txt:md5,2a2d04e030d228b9e6c3267e6f9e6225", + "mapping_quality_across_reference.txt:md5,33942e63dd23b4c0e307cd2f8c2fb299", + "mapping_quality_histogram.txt:md5,5d14a661b9d3d59e4dfcb841084a6def", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + 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"duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8", + "genome_fraction_coverage.txt:md5,ca40e719b074696357494e3cba520d4a", + "mapped_reads_gc-content_distribution.txt:md5,4927664b2fcd95fe01daeb1315fffdf7", + "mapped_reads_nucleotide_content.txt:md5,ffdced213cd2a96408c4b9794092bd80", + "mapping_quality_across_reference.txt:md5,a15709e1860fdd7deaf86dfa0d461144", + "mapping_quality_histogram.txt:md5,feafb188d85e486d16374117565d88d1", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", 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"coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce", + "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301", + "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b", + "genome_fraction_coverage.txt:md5,48f654e7179fdb7c4830ceb8f862af0b", + "mapped_reads_gc-content_distribution.txt:md5,a603a3d326e811f38f448cd3d017b4a8", + "mapped_reads_nucleotide_content.txt:md5,783a0fb23148a56c1c78a21d774109eb", + "mapping_quality_across_reference.txt:md5,d9bafb5cc106bbd1dc7e31439c618f19", + "mapping_quality_histogram.txt:md5,560e85b88f5f90e9ad7ad93ffef42d6f" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-21T12:52:21.997483371" + "timestamp": "2024-09-22T11:59:47.304646324" } } \ No newline at end of file diff --git a/tests/default.nf.test b/tests/default.nf.test index 8787c641..79f0411e 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,73 +12,29 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - bam("$outputDir/bismark/deduplicated/Ecoli.deduplicated.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam").getReadsMD5(), - bam("$outputDir/bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam").getReadsMD5(), - path("$outputDir/bismark/deduplicated/Ecoli.deduplicated.sorted.bam.bai"), - path("$outputDir/bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai"), - path("$outputDir/bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai"), - path("$outputDir/bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.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("Default") }, + // Number of tasks + workflow.trace.tasks().size(), - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/Ecoli_1_val_1_bismark_bt2_pe.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/deduplicated/logs/SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/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("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/Ecoli_1_val_1_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/Ecoli_2_val_2_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/SRR389222_sub1_trimmed_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/SRR389222_sub2_trimmed_fastqc.html").exists() }, - { assert new File("$outputDir/trimgalore/fastqc/SRR389222_sub3_trimmed_fastqc.html").exists() }, - { assert new File("$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() }, + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + // All stable path name + stable_name*.name, + + // All files with stable contents + stable_path + ).match() } ) + } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f42db2b4..1511e295 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,6 +1,7 @@ { - "software_versions": { + "Default": { "content": [ + 47, { "BISMARK_ALIGN": { "bismark": "0.24.0" @@ -21,33 +22,475 @@ "Workflow": { "nf-core/methylseq": "v2.7.0dev" } - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-21T13:00:28.283819613" - }, - "Default": { - "content": [ - "a54ab7c96f9523a4ccd25fd69f6905f8", - "3f11ef5fbbda3797fd6217728e4f00d3", - "b01f29fc1d8d46922a69df09c636b4c4", - "347195c04c9ffd2a2b10967a6682fc69", - "Ecoli.deduplicated.sorted.bam.bai:md5,26fc8064684ace3d1e1dc93436f7ccb2", - "SRR389222_sub1.deduplicated.sorted.bam.bai:md5,9c16bbc7317764c83d6b1a6c53a24e6e", - "SRR389222_sub2.deduplicated.sorted.bam.bai:md5,d6f8dd9bd45aa9374e432d1640fa5453", - "SRR389222_sub3.deduplicated.sorted.bam.bai:md5,8dda4abae921786e8b099b048121fc3d", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,d31df76c1c9128299367ebfe740357b9", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,010f32001bbc7805f8e041f3ef0d9ea9", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,d42e09af121ae14f6e0de5779e317b0b", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,ed28b3cce432eecfae73bc4a071ec4ee", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b06ce0084e54193ff8c9b9dd0ec9757b", - "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b865b7fb6e1225feeb6aef3372ef0b1d", + }, [ + "bismark", + "alignments", + "logs", + "Ecoli_1_val_1_bismark_bt2_PE_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "deduplicated", + "Ecoli.deduplicated.sorted.bam", + "Ecoli.deduplicated.sorted.bam.bai", + "SRR389222_sub1.deduplicated.sorted.bam", + "SRR389222_sub1.deduplicated.sorted.bam.bai", + "SRR389222_sub2.deduplicated.sorted.bam", + "SRR389222_sub2.deduplicated.sorted.bam.bai", + "SRR389222_sub3.deduplicated.sorted.bam", + "SRR389222_sub3.deduplicated.sorted.bam.bai", + "logs", + "Ecoli_1_val_1_bismark_bt2_pe.deduplication_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt", + "methylation_calls", + "bedGraph", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "mbias", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "methylation_calls", + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "methylation_coverage", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "splitting_report", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "reports", + "Ecoli_1_val_1_bismark_bt2_PE_report.html", + "SRR389222_sub1_trimmed_bismark_bt2_SE_report.html", + "SRR389222_sub2_trimmed_bismark_bt2_SE_report.html", + "SRR389222_sub3_trimmed_bismark_bt2_SE_report.html", + "summary", + "bismark_summary_report.html", + "bismark_summary_report.txt", + "fastqc", + "Ecoli_1_fastqc.html", + "Ecoli_2_fastqc.html", + "SRR389222_sub1_fastqc.html", + "SRR389222_sub2_fastqc.html", + "SRR389222_sub3_fastqc.html", + "zips", + "Ecoli_1_fastqc.zip", + "Ecoli_2_fastqc.zip", + "SRR389222_sub1_fastqc.zip", + "SRR389222_sub2_fastqc.zip", + "SRR389222_sub3_fastqc.zip", + "multiqc", + "bismark", + "multiqc_data", + "bismark-methylation-dp.txt", + "bismark_alignment.txt", + "bismark_deduplication.txt", + "bismark_mbias_CHG_R1.txt", + "bismark_mbias_CHG_R2.txt", + "bismark_mbias_CHH_R1.txt", + "bismark_mbias_CHH_R2.txt", + "bismark_mbias_CpG_R1.txt", + "bismark_mbias_CpG_R2.txt", + "bismark_strand_alignment.txt", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "multiqc.log", + "multiqc_bismark_alignment.txt", + "multiqc_bismark_dedup.txt", + "multiqc_bismark_methextract.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_qualimap_bamqc_genome_results.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "qualimap_coverage_histogram.txt", + "qualimap_gc_content.txt", + "qualimap_genome_fraction.txt", + "qualimap_insert_size.txt", + "multiqc_plots", + "pdf", + "bismark-methylation-dp.pdf", + "bismark_alignment-cnt.pdf", + "bismark_alignment-pct.pdf", + "bismark_deduplication-cnt.pdf", + "bismark_deduplication-pct.pdf", + "bismark_mbias_CHG_R1.pdf", + "bismark_mbias_CHG_R2.pdf", + "bismark_mbias_CHH_R1.pdf", + "bismark_mbias_CHH_R2.pdf", + "bismark_mbias_CpG_R1.pdf", + "bismark_mbias_CpG_R2.pdf", + "bismark_strand_alignment-cnt.pdf", + "bismark_strand_alignment-pct.pdf", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_adapter_content_plot.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "general_stats_table.pdf", + "qualimap_coverage_histogram.pdf", + "qualimap_gc_content.pdf", + "qualimap_genome_fraction.pdf", + "qualimap_insert_size.pdf", + "png", + "bismark-methylation-dp.png", + "bismark_alignment-cnt.png", + "bismark_alignment-pct.png", + "bismark_deduplication-cnt.png", + "bismark_deduplication-pct.png", + "bismark_mbias_CHG_R1.png", + "bismark_mbias_CHG_R2.png", + "bismark_mbias_CHH_R1.png", + "bismark_mbias_CHH_R2.png", + "bismark_mbias_CpG_R1.png", + "bismark_mbias_CpG_R2.png", + "bismark_strand_alignment-cnt.png", + "bismark_strand_alignment-pct.png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "fastqc-status-check-heatmap.png", + "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_top_overrepresented_sequences_table.png", + "general_stats_table.png", + "qualimap_coverage_histogram.png", + "qualimap_gc_content.png", + "qualimap_genome_fraction.png", + "qualimap_insert_size.png", + "svg", + "bismark-methylation-dp.svg", + "bismark_alignment-cnt.svg", + "bismark_alignment-pct.svg", + "bismark_deduplication-cnt.svg", + "bismark_deduplication-pct.svg", + "bismark_mbias_CHG_R1.svg", + "bismark_mbias_CHG_R2.svg", + "bismark_mbias_CHH_R1.svg", + "bismark_mbias_CHH_R2.svg", + "bismark_mbias_CpG_R1.svg", + "bismark_mbias_CpG_R2.svg", + "bismark_strand_alignment-cnt.svg", + "bismark_strand_alignment-pct.svg", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.svg", + "cutadapt_trimmed_sequences_plot_3_Counts.svg", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "fastqc-status-check-heatmap.svg", + "fastqc_adapter_content_plot.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg", + 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b/tests/lib/UTILS.groovy index 73652fb9..48500bd3 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -1,11 +1,23 @@ -// Function to remove Nextflow version from software_versions.yml - class UTILS { - public static Object removeNextflowVersion(outputDir) { - def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } + // Remove Nextflow version from pipeline_software_mqc_versions.yml + public static Object removeNextflowVersion(pipeline_software_mqc_versions) { + def softwareVersions = path(pipeline_software_mqc_versions).yaml + if (softwareVersions.containsKey("Workflow")) softwareVersions.Workflow.remove("Nextflow") return softwareVersions } + + // Recursively list all files in a directory and its sub-directories, matching or not matching supplied suffixes + public static getAllFilesFromDir(outdir, boolean includeDir = true, List excludeRegexes = null) { + def output = [] + new File(outdir).eachFileRecurse() { file -> + boolean matchesInclusion = includeDir ? true : file.isFile() + boolean matchesExclusion = excludeRegexes ? excludeRegexes.any { regex -> file.name.toString() ==~ regex } : false + + // Add files (or folders if includeDir is set to true) to the list that don't match excludeRegexes + if (matchesInclusion && !matchesExclusion) output.add(file) + } + return output.sort { it.path } + } + // Static (global) exclusion regexes list + static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] } diff --git a/tests/lib/UTILS_PIPELINE.groovy b/tests/lib/UTILS_PIPELINE.groovy new file mode 100644 index 00000000..fce45f23 --- /dev/null +++ b/tests/lib/UTILS_PIPELINE.groovy @@ -0,0 +1,74 @@ +class UTILS_PIPELINE { + // These are the files to exclude when we want to snapshot + static List exclusionRegexesForUnstableFileContents = [ + + // To exlude Bismark reports + /.*_report\.txt/, + /bismark_summary_report\.html/, + /.*_report\.html/, + + // To exclude the pipeline_software_mqc_versions.yml file that contains the Nextflow version + /nf_core_.*_software_mqc_versions\.yml/, + + // To exclude this folder that somehow is a file on stub tests + /multiqc_plots/, + + // To exclude FASTQC reports + /.*_raw\.(html|zip)/, + /.*_fastqc\.(html|zip)/, + + // To exclude from the MultiQC reports + /bismark_alignment-(cnt|pct)\.(pdf|svg)/, + /bismark_deduplication-(cnt|pct)\.(pdf|svg)/, + /bismark-methylation-dp\.(pdf|svg|png)/, + /bismark_mbias_CHG_R1\.(pdf|svg)/, + /bismark_mbias_CHG_R2\.(pdf|svg)/, + /bismark_mbias_CHH_R1\.(pdf|svg)/, + /bismark_mbias_CHH_R2\.(pdf|svg)/, + /bismark_mbias_CpG_R1\.(pdf|svg)/, + /bismark_mbias_CpG_R2\.(pdf|svg)/, + /bismark_strand_alignment-(cnt|pct)\.(pdf|svg)/, + /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/, + /cutadapt_trimmed_sequences_plot_3_Counts\.(pdf|svg)/, + /cutadapt_trimmed_sequences_plot_3_Obs_Exp\.(pdf|svg)/, + /qualimap_coverage_histogram-(cnt|pct)\.(pdf|svg)/, + /fastqc_adapter_content_plot\.(pdf|png|svg)/, + /fastqc_overrepresented_sequences_plot(.*)?\.(pdf|svg)/, + /fastqc_per_base_.*_plot(.*)?\.(pdf|png|svg)/, + /fastqc_per_sequence_.*\.(pdf|svg)/, + /fastqc_sequence_(counts|duplication_levels)_plot(.*)?\.(pdf|svg)/, + /fastqc-status-check-.*\.(pdf|svg)/, + /fastqc_top_overrepresented_sequences_table(.*)?\.(pdf|png|svg|txt)/, + /fastqc_adapter_content_plot\.(pdf|png|svg)/, + /fastqc_overrepresented_sequences_plot(.*)?\.(pdf|svg)/, + /general_stats_table\.(pdf|png|svg)/, + /qualimap_coverage_histogram\.(pdf|svg)/, + /qualimap_gc_content\.(pdf|svg)/, + /qualimap_genome_fraction\.(pdf|svg)/, + /qualimap_insert_size\.(pdf|svg)/, + /multiqc_data\.json/, + /multiqc\.log/, + /multiqc_sources\.txt/, + /multiqc_fastqc\.txt/, + /multiqc_fail_strand_check_table\.txt/, + /multiqc_general_stats\.txt/, + + // To exclude Picard Markduplicates metrics + /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, + + // To exclude Qualimap files + /.*\.(css|gif|js)/, + /images_qualimapReport/, + /raw_data_qualimapReport/, + /qualimapReport\.html/, + + // To exclude from samtools stats + /.*\.sorted\.bam\.(flagstat|idxstats|stats)/, + + // To exclude markdup + /.*\.markdup\.sorted\.bam(\.bai)?/, + + // To exclude trimgalore + /.*\.fastq\.gz_trimming_report\.txt/ + ] +}