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GallVpGallVp
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Updated snapshots and added a test
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+153
-5
lines changed

3 files changed

+153
-5
lines changed

‎tests/hic/main.nf.test

Lines changed: 53 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -54,4 +54,57 @@ nextflow_pipeline {
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}
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test("hic - HY - test - assembly") {
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when {
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params {
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input = "$baseDir/tests/hic/assemblysheet.csv"
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hic = "$baseDir/tests/hic/testdata/HYh1h2_Chr01_6000000_6015000.R{1,2}.fastq.gz"
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hic_assembly_mode = true
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hic_juicer_tools_pre_ext_args = '-n'
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outdir = "$outputDir"
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}
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}
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then {
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def stable_path = getAllFilesFromDir(
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params.outdir,
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false,
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[
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'pipeline_info/*.{html,json,txt,yml}',
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'hic/fastp/*.fastq.gz',
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'hic/fastp/*.html',
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'hic/fastp/*.log',
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'hic/hicqc/*.pdf',
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'report.{html,json}'
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],
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null,
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['**']
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)
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def stable_name = getAllFilesFromDir(
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params.outdir,
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true,
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[
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'pipeline_info/*.{html,json,txt,yml}'
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],
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null,
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['**']
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)
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assertAll(
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{ assert workflow.success},
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{ assert snapshot(
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[
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'successful tasks': workflow.trace.succeeded().size(),
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'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"),
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'stable paths': stable_path,
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'stable names': getRelativePath(stable_name, outputDir),
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]
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).match() }
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)
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}
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}
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}

‎tests/hic/main.nf.test.snap

Lines changed: 97 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,99 @@
11
{
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"hic - HY - test - assembly": {
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"content": [
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{
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"successful tasks": 18,
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"versions": {
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"ASSEMBLATHON_STATS": {
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"assemblathon_stats": "github/PlantandFoodResearch/assemblathon2-analysis/a93cba2"
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},
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"BWA_INDEX": {
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"bwa": "0.7.18-r1243-dirty"
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},
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"BWA_MEM": {
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"bwa": "0.7.18-r1243-dirty",
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"samtools": 1.21
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},
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"FALINT": {
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"fa-lint": "1.1.0"
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},
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"FASTP": {
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"fastp": "0.24.0"
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},
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"GUNZIP_FASTA": {
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"gunzip": 1.13
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},
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"HIC2HTML": {
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"python": "3.11.3"
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},
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"HICQC": {
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"hic_qc.py": "1.3.1"
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},
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"JUICEBOXSCRIPTS_MAKEAGPFROMFASTA": {
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"juicebox_scripts": "0.1.0"
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},
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"JUICERTOOLS_PRE": {
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"juicertools": "2.20.00"
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},
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"SAMBLASTER": {
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"samblaster": "0.1.26",
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"samtools": "1.19.2"
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},
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"SAMTOOLS_FAIDX": {
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"samtools": 1.21
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},
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"SEQKIT_RMDUP": {
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"seqkit": "v2.9.0"
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},
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"SEQKIT_SORT": {
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"seqkit": "v2.9.0"
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},
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"TAG_ASSEMBLY": {
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"pigz": "2.3.4"
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},
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"Workflow": {
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"plant-food-research-open/assemblyqc": "v3.0.0dev"
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},
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"YAHS_JUICERPRE": {
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"yahs": "1.2.2"
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}
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},
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"stable paths": [
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"HY_stats.csv:md5,fc61def49f669e7b3f885bf2555bcd46",
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"HY.assembly:md5,2154e1e2f2c12dd43765bc35a2003826",
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"HY.assembly.agp:md5,1389ded06e1056dd03d44a849788c4ad",
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"HY.hic:md5,171b1a467890960d0e5e16ebf13f9ce9",
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"HY.html:md5,074daab0df3a1352a1a263395b66d6c1",
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"HYh1h2_Chr01_6000000_6015000.R.fastp.json:md5,0f757d8f9e7b1fcf8cee5b18127ee02d"
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],
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"stable names": [
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"assemblathon_stats",
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"assemblathon_stats/HY_stats.csv",
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"hic",
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"hic/HY.assembly",
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"hic/HY.assembly.agp",
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"hic/HY.hic",
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"hic/HY.html",
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"hic/fastp",
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"hic/fastp/HYh1h2_Chr01_6000000_6015000.R.fastp.html",
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"hic/fastp/HYh1h2_Chr01_6000000_6015000.R.fastp.json",
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"hic/fastp/HYh1h2_Chr01_6000000_6015000.R.fastp.log",
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"hic/hicqc",
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"hic/hicqc/HY_qc_report.pdf",
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"pipeline_info",
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"report.html",
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"report.json",
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"synteny",
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"synteny/plotsr"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.2"
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},
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"timestamp": "2025-06-18T18:58:15.972463"
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},
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"hic - HY - test": {
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"content": [
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{
@@ -27,7 +122,7 @@
27122
"python": "3.11.3"
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},
29124
"HICQC": {
30-
"hic_qc.py": 1.3
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"hic_qc.py": "1.3.1"
31126
},
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"JUICEBOXSCRIPTS_MAKEAGPFROMFASTA": {
33128
"juicebox_scripts": "0.1.0"
@@ -91,6 +186,6 @@
91186
"nf-test": "0.9.2",
92187
"nextflow": "25.04.2"
93188
},
94-
"timestamp": "2025-06-11T09:52:03.812486"
189+
"timestamp": "2025-06-18T18:51:07.785869"
95190
}
96191
}

‎tests/stub/main.nf.test.snap

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -96,7 +96,7 @@
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"python": "3.11.3"
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},
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"HICQC": {
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"hic_qc.py": 1.3
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"hic_qc.py": "1.3.1"
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},
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"JUICEBOXSCRIPTS_MAKEAGPFROMFASTA": {
102102
"juicebox_scripts": "0.1.0"
@@ -293,6 +293,6 @@
293293
"nf-test": "0.9.2",
294294
"nextflow": "25.04.2"
295295
},
296-
"timestamp": "2025-06-06T15:19:38.285789"
296+
"timestamp": "2025-06-18T18:49:43.239383"
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}
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}
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}

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