From b5c3b27d95e5ffaff51bbb5f2747b96ec0501449 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Mon, 30 Sep 2024 15:36:55 +0200 Subject: [PATCH] Added miniseq bclconvert test --- conf/test_bclconvert.config | 27 +++++++ nextflow.config | 2 +- tests/pipeline/bclconvert_mini.nf.test | 55 ++++++++++++++ tests/pipeline/bclconvert_mini.nf.test.snap | 83 +++++++++++++++++++++ 4 files changed, 166 insertions(+), 1 deletion(-) create mode 100755 conf/test_bclconvert.config create mode 100644 tests/pipeline/bclconvert_mini.nf.test create mode 100644 tests/pipeline/bclconvert_mini.nf.test.snap diff --git a/conf/test_bclconvert.config b/conf/test_bclconvert.config new file mode 100755 index 00000000..d9b91ed1 --- /dev/null +++ b/conf/test_bclconvert.config @@ -0,0 +1,27 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/demultiplex -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +params { + config_profile_name = 'Test bclconvert profile' + config_profile_description = 'Minimal test dataset to check bclconvert pipeline function' + + // Limit resources so that this can run on GitHub Actions + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' + + // Input data + input = 'https://huggingface.co/datasets/nf-core/demultiplex/resolve/main/testdata/Miniseq_truseq_smrna/input_samplesheet.csv' + demultiplexer = 'bclconvert' + skip_tools = 'samshee' + +} diff --git a/nextflow.config b/nextflow.config index c018a819..b49efe72 100755 --- a/nextflow.config +++ b/nextflow.config @@ -200,7 +200,7 @@ profiles { test_pe { includeConfig 'conf/test_pe.config' } test_bases2fastq { includeConfig 'conf/test_bases2fastq.config' } test_bcl2fastq { includeConfig 'conf/test_bcl2fastq.config' } - test_bclconvert { includeConfig 'conf/test.config' } + test_bclconvert { includeConfig 'conf/test_bclconvert.config' } test_full { includeConfig 'conf/test_full.config' } test_sgdemux { includeConfig 'conf/test_sgdemux.config' } test_fqtk { includeConfig 'conf/test_fqtk.config' } diff --git a/tests/pipeline/bclconvert_mini.nf.test b/tests/pipeline/bclconvert_mini.nf.test new file mode 100644 index 00000000..6f947349 --- /dev/null +++ b/tests/pipeline/bclconvert_mini.nf.test @@ -0,0 +1,55 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - BCLCONVERT-mini" + script "main.nf" + profile "test_bclconvert" + tag "bclconvert" + tag "pipeline" + + test("BCL-CONVERT-mini") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 26 }, + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/bclconvert_lane_counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/bclconvert_sample_counts_Counts_per_lane.txt") + ).match("multiqc") }, + { assert snapshot( + path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001.fastp.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/HBRR1_S1_L001_summary.txt"), + path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001.fastp.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/HBRR2_S2_L001_summary.txt"), + path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001.fastp.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/HBRR3_S3_L001_summary.txt"), + path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001.fastp.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/UHRR1_S4_L001_summary.txt"), + path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001.fastp.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/UHRR2_S5_L001_summary.txt"), + path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001.fastp.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/UHRR3_S6_L001_summary.txt"), + path("$outputDir/miniseq_truseq_smrna/Undetermined_S0_L001_R1_001.fastq.gz"), + path("$outputDir/miniseq_truseq_smrna/Reports/").list(), + path("$outputDir/miniseq_truseq_smrna/InterOp/").list() + ).match("bclconvert") } + ) + } + + } + +} diff --git a/tests/pipeline/bclconvert_mini.nf.test.snap b/tests/pipeline/bclconvert_mini.nf.test.snap new file mode 100644 index 00000000..0f520c83 --- /dev/null +++ b/tests/pipeline/bclconvert_mini.nf.test.snap @@ -0,0 +1,83 @@ +{ + "bclconvert": { + "content": [ + "HBRR1_S1_L001.fastp.fastq.gz:md5,451657490d4816dd5ff904e34ecc7fdf", + "HBRR1_S1_L001_R1_001.fastq.gz:md5,451657490d4816dd5ff904e34ecc7fdf", + "HBRR1_S1_L001_summary.txt:md5,53a5e6bac1e853f23d27d6966e52df81", + "HBRR2_S2_L001.fastp.fastq.gz:md5,3b9e4fc70ebc608b48d1f0027265e9b8", + "HBRR2_S2_L001_R1_001.fastq.gz:md5,3b9e4fc70ebc608b48d1f0027265e9b8", + "HBRR2_S2_L001_summary.txt:md5,f3e0bc27d30d0f6e10ad76be47017881", + "HBRR3_S3_L001.fastp.fastq.gz:md5,a110eefaee1da4d99398500e55919f0c", + "HBRR3_S3_L001_R1_001.fastq.gz:md5,a110eefaee1da4d99398500e55919f0c", + "HBRR3_S3_L001_summary.txt:md5,fbe9c4281a768a826429e328f5eb2a34", + "UHRR1_S4_L001.fastp.fastq.gz:md5,03f215bcb4005804f60acccfe4aaef78", + "UHRR1_S4_L001_R1_001.fastq.gz:md5,b470c82d2002c563c42786060ae364b9", + "UHRR1_S4_L001_summary.txt:md5,c6c342cbcad3fc68343284c24e4a8b4a", + "UHRR2_S5_L001.fastp.fastq.gz:md5,2186d5f37865f970d223953e9a5412ae", + "UHRR2_S5_L001_R1_001.fastq.gz:md5,47c36adf557bf4d37b0a84d055125290", + "UHRR2_S5_L001_summary.txt:md5,121a0aeaf860fae497a27e8eceff3283", + "UHRR3_S6_L001.fastp.fastq.gz:md5,674c4989c2270d88612fcf221e3e0950", + "UHRR3_S6_L001_R1_001.fastq.gz:md5,bdb407e3ded3691479ec25f5f1df3b07", + "UHRR3_S6_L001_summary.txt:md5,d7d5a014b51d64e4da1a113a4ad79eda", + "Undetermined_S0_L001_R1_001.fastq.gz:md5,b0b4daae001636cf033ff760a5ab479d", + [ + "Adapter_Cycle_Metrics.csv:md5,757778bb0ee048463c423dff14133a51", + "Adapter_Metrics.csv:md5,5cbba841c650097f1e759c2b75c7a005", + "Demultiplex_Stats.csv:md5,40c3efd7ffb9d02fcc97028f6ee98c96", + "Demultiplex_Tile_Stats.csv:md5,916e3e488c4ed847249d7d46401a57ff", + "IndexMetricsOut.bin:md5,9a6ad90fd45b3abd2360285feff76509", + "Index_Hopping_Counts.csv:md5,1059369e375fd8f8423c0f6c934be978", + "Quality_Metrics.csv:md5,215e001631d9383f73360975d5726f14", + "Quality_Tile_Metrics.csv:md5,122f967d30318f79f5a7ef59339f8275", + "RunInfo.xml:md5,d3d94b916915b35224ec362c64542190", + "SampleSheet.csv:md5,c32433167a5c56d5c15952c2e7948898", + "Top_Unknown_Barcodes.csv:md5,b5fa3ea9ba12fd35650e36e6c5cbdc99", + "fastq_list.csv:md5,07cbe4173e18cbdef16ee8feb4adaf7d" + ], + [ + "CorrectedIntMetricsOut.bin:md5,4d82e208f18bfd51a5f9275e05d073ba", + "EmpiricalPhasingMetricsOut.bin:md5,0e9d6b71c90661d800b1129a0097c301", + "ErrorMetricsOut.bin:md5,dbc41ced845d7645451c6995e5774c0b", + "EventMetricsOut.bin:md5,5a93a812df6a55e6d7a0f26bdf176e93", + "ExtendedTileMetricsOut.bin:md5,5ffaee26c4ed0074f69d8c62293118f9", + "ExtractionMetricsOut.bin:md5,a4d4c0d3b9afe453fae7ca6118c9346d", + "FWHMGridMetricsOut.bin:md5,80e7c3652f72edbc5f661a1f1b3b28fc", + "ImageMetricsOut.bin:md5,2dddf68f924261ab37f83e8ee750b6f2", + "IndexMetricsOut.bin:md5,e63ea5cfa848feab8a40ba469ff46845", + "PFGridMetricsOut.bin:md5,e65fed6f9594655657521a5359759b01", + "QMetrics2030Out.bin:md5,670b3c089d4d264103a01105d12abbe8", + "QMetricsByLaneOut.bin:md5,b6d8d8ff4144f33a3f4304743db53f97", + "QMetricsOut.bin:md5,13fee543cefb5d5ae1c108ccbb07f0e6", + "RegistrationMetricsOut.bin:md5,b201979275957afbbcea634698afc352", + "TileMetricsOut.bin:md5,0d2aa2c7e39eb33e61d2ed248068ed9d" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:27:18.543806" + }, + "software_versions": { + "content": [ + "{BCLCONVERT={bclconvert=4.3.6}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, Workflow={nf-core/demultiplex=v1.5.1}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:27:18.472169" + }, + "multiqc": { + "content": [ + "bclconvert_lane_counts.txt:md5,7c8bdcf459b8900c88f3426a324a9368", + "fastp_filtered_reads_plot.txt:md5,181ce851d1ab86f434b12082e8513ec4", + "bclconvert_sample_counts_Counts_per_lane.txt:md5,76cf037883c6c8b71ac5fa181a41fec6" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:27:18.49554" + } +} \ No newline at end of file