From 9be68d909607e56be2c9b51ee6684c3ae4c5795a Mon Sep 17 00:00:00 2001 From: Sateesh Date: Mon, 4 Nov 2024 11:10:06 +0000 Subject: [PATCH] add bwameth_gpu nf-test + snap --- assets/samplesheet_gpu.csv | 4 + tests/bwameth_gpu.nf.test | 61 ++++++ tests/bwameth_gpu.nf.test.snap | 338 +++++++++++++++++++++++++++++++++ tests/gpu.config | 42 ++++ 4 files changed, 445 insertions(+) create mode 100644 assets/samplesheet_gpu.csv create mode 100644 tests/bwameth_gpu.nf.test create mode 100644 tests/bwameth_gpu.nf.test.snap create mode 100644 tests/gpu.config diff --git a/assets/samplesheet_gpu.csv b/assets/samplesheet_gpu.csv new file mode 100644 index 00000000..fb599e76 --- /dev/null +++ b/assets/samplesheet_gpu.csv @@ -0,0 +1,4 @@ +sample,fastq_1,fastq_2,genome +SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, +SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, +SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, diff --git a/tests/bwameth_gpu.nf.test b/tests/bwameth_gpu.nf.test new file mode 100644 index 00000000..8b822126 --- /dev/null +++ b/tests/bwameth_gpu.nf.test @@ -0,0 +1,61 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./gpu.config" + + test("Params: bwameth") { + when { + params { + aligner = "bwameth" + use_gpu = true + outdir = "$outputDir" + } + } + + 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() } + ) + } + } + + test("Params: bwameth with bwameth-index") { + when { + params { + aligner = "bwameth" + bwameth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size() + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_gpu.nf.test.snap b/tests/bwameth_gpu.nf.test.snap new file mode 100644 index 00000000..2b98ab69 --- /dev/null +++ b/tests/bwameth_gpu.nf.test.snap @@ -0,0 +1,338 @@ +{ + "Params: bwameth": { + "content": [ + 38, + { + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "PARABRICKS_FQ2BAMMETH": { + "pbrun": "4.3.2-1" + }, + "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/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", + 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"samtools-flagstat-dp_Percentage_of_total.txt:md5,921b0c969e7c154c0cd18b331e2a6c1c", + "samtools-flagstat-dp_Read_counts.txt:md5,c0764320e38e62b48d59f608094804b8", + "samtools-stats-dp.txt:md5,99418ae30d5855a3d8cd9cfdf21dd14d", + "samtools_alignment_plot.txt:md5,34b8fa8a88b6f5ef00153b07aabc028d", + "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", + "genome_results.txt:md5,2294badeccd2e8870fd6c60d115687b0", + "genome_results.txt:md5,4da1144933d094185d02f7482c120804" + ], + [ + [ + "SRR389222_sub1.markdup.sorted.bam", + "97e6767c5ddea54cb2a6498192a09c68" + ], + [ + "SRR389222_sub2.markdup.sorted.bam", + "313ae71af4023059a295ed8a132fd9ad" + ], + [ + "SRR389222_sub3.markdup.sorted.bam", + "9eaa07df5ad58a78ab57ee55f948a044" + ] + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T10:50:08.152373" + }, + "Params: bwameth with bwameth-index": { + "content": [ + 38 + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-04T10:51:07.793352" + } +} diff --git a/tests/gpu.config b/tests/gpu.config new file mode 100644 index 00000000..cfd0b5b9 --- /dev/null +++ b/tests/gpu.config @@ -0,0 +1,42 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + // Base directory for nf-core/modules test data + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + // Base directory for nf-core/methylseq test data + pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/methylseq/' + + // Input data + input = "${projectDir}/assets/samplesheet_gpu.csv" + fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa" + fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai" + outdir = 'results' +} + +// Impose sensible resource limits for testing +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } + + withName: PRESEQ_LCEXTRAP { + errorStrategy = 'ignore' + } +} + +// Impose same minimum Nextflow version as the pipeline for testing +manifest { + nextflowVersion = '!>=24.04.2' +} + +// Disable all Nextflow reporting options +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false }