From 754065d7d39de26548f76e2fa01f58608ac175ed Mon Sep 17 00:00:00 2001 From: Sateesh Date: Mon, 2 Dec 2024 12:47:16 +0000 Subject: [PATCH] add bwameth run_qualimap test --- tests/.nftignore | 2 +- tests/bismark_run_qualimap.nf.test.snap | 8 +- tests/bwameth_run_qualimap.nf.test | 42 ++ tests/bwameth_run_qualimap.nf.test.snap | 586 ++++++++++++++++++++++++ 4 files changed, 631 insertions(+), 7 deletions(-) create mode 100644 tests/bwameth_run_qualimap.nf.test create mode 100644 tests/bwameth_run_qualimap.nf.test.snap diff --git a/tests/.nftignore b/tests/.nftignore index 7c0558cf..5c3f0a21 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -14,7 +14,7 @@ multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_sources.txt multiqc/{bismark,bismark_hisat,bwameth}/multiqc_report.html multiqc/{bismark,bismark_hisat,bwameth}/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg} pipeline_info/*.{html,json,txt,yml} -qualimap/**/qualimapReport.html +{bismark,bismark_hisat,bwameth}/qualimap/bamqc/*/qualimapReport.html qualimap/**/css/* qualimap/**/images_qualimapReport/* qualimap/**/raw_data_qualimapReport/* diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap index ba30b070..78214c46 100644 --- a/tests/bismark_run_qualimap.nf.test.snap +++ b/tests/bismark_run_qualimap.nf.test.snap @@ -556,7 +556,6 @@ "genome_mapping_quality_histogram.png:md5,74776b1e7e8c8876af1cf89d9dbb5f31", "genome_reads_content_per_read_position.png:md5,c6920dc357411880132c207c7d0aa68d", "genome_uniq_read_starts_histogram.png:md5,8f7549a63eee3d3f022699aaa5bb858d", - "qualimapReport.html:md5,bbc015c0d1f3c41a08c82fb7a6839039", "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4", "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e", "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25", @@ -601,7 +600,6 @@ "genome_mapping_quality_histogram.png:md5,7ba0db9375d09fd49946b9bca4ba92b4", "genome_reads_content_per_read_position.png:md5,1a6a7717ea948d2518808f72f58ffdef", "genome_uniq_read_starts_histogram.png:md5,395413ab1d0e10af72b116fd8cb12685", - "qualimapReport.html:md5,1fe626f663d66a7ce0c6e1e0207d829d", "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803", "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2", "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1", @@ -643,7 +641,6 @@ "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956", "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157", "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19", - "qualimapReport.html:md5,af640b29bd28f80bdc0ab6fe7d9c97f4", "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2", "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80", "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8", @@ -685,7 +682,6 @@ "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92", "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de", "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03", - "qualimapReport.html:md5,c8114fbb2a63da68111f0d4cbb8a1973", "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce", "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301", "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b", @@ -752,6 +748,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-11-28T09:47:26.992492832" + "timestamp": "2024-12-02T12:34:53.964190449" } -} +} \ No newline at end of file diff --git a/tests/bwameth_run_qualimap.nf.test b/tests/bwameth_run_qualimap.nf.test new file mode 100644 index 00000000..5f671e42 --- /dev/null +++ b/tests/bwameth_run_qualimap.nf.test @@ -0,0 +1,42 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bwameth | run_qualimap") { + when { + params { + aligner = "bwameth" + outdir = "$outputDir" + run_qualimap = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_run_qualimap.nf.test.snap b/tests/bwameth_run_qualimap.nf.test.snap new file mode 100644 index 00000000..cc1376a2 --- /dev/null +++ b/tests/bwameth_run_qualimap.nf.test.snap @@ -0,0 +1,586 @@ +{ + "Params: bwameth | run_qualimap": { + "content": [ + 51, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9 + }, + "Workflow": { + "nf-core/methylseq": "v2.8.0dev" + } + }, + [ + "bwameth", + "bwameth/alignments", + "bwameth/alignments/samtools_stats", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub1.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", + "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", + "bwameth/deduplicated/picard_metrics", + "bwameth/deduplicated/picard_metrics/Ecoli_10K_methylated.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/qualimap", + "bwameth/qualimap/bamqc", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/agogo.css", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/ajax-loader.gif", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/basic.css", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/bgfooter.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/bgtop.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/comment-bright.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/comment-close.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/comment.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/doctools.js", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/down-pressed.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/down.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/file.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/jquery.js", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/minus.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/css/plus.png", + 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"bwameth/qualimap/bamqc/Ecoli_10K_methylated/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/qualimapReport.html", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/coverage_across_reference.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/coverage_histogram.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/duplication_rate_histogram.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/genome_fraction_coverage.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/homopolymer_indels.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/insert_size_across_reference.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/insert_size_histogram.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "bwameth/qualimap/bamqc/Ecoli_10K_methylated/raw_data_qualimapReport/mapping_quality_histogram.txt", + "bwameth/qualimap/bamqc/SRR389222_sub1", + "bwameth/qualimap/bamqc/SRR389222_sub1/css", + "bwameth/qualimap/bamqc/SRR389222_sub1/css/agogo.css", + "bwameth/qualimap/bamqc/SRR389222_sub1/css/ajax-loader.gif", + "bwameth/qualimap/bamqc/SRR389222_sub1/css/basic.css", + "bwameth/qualimap/bamqc/SRR389222_sub1/css/bgfooter.png", + "bwameth/qualimap/bamqc/SRR389222_sub1/css/bgtop.png", + "bwameth/qualimap/bamqc/SRR389222_sub1/css/comment-bright.png", + 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