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Merge pull request #267 from nschcolnicov/add_bclconvert_test
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Added miniseq bclconvert test
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@apeltzer
apeltzer authored Sep 30, 2024
2 parents 3562e9e + b5c3b27 commit 73df4a5
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Showing 4 changed files with 166 additions and 1 deletion.
27 changes: 27 additions & 0 deletions conf/test_bclconvert.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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,<docker/singularity> --outdir <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'

}
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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' }
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55 changes: 55 additions & 0 deletions tests/pipeline/bclconvert_mini.nf.test
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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") }
)
}

}

}
83 changes: 83 additions & 0 deletions tests/pipeline/bclconvert_mini.nf.test.snap
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{
"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"
}
}

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