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Daniel-VMDaniel-VM
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Merge pull request #260 from Daniel-VM/dev
Fix unestable files when nf-tests run using conda
2 parents 954f51e + 9fd9c1d commit d46987d

11 files changed

+23
-194
lines changed

‎CHANGELOG.md‎

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@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Fixed`
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- [#260](https://github.com/nf-core/bacass/pull/260) Fix unestable files when nf-tests run using conda.
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- [#258](https://github.com/nf-core/bacass/pull/258) Update and Fix ToulligQC.
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- [#256](https://github.com/nf-core/bacass/pull/256) Update module busco to avoid version number error when using conda.
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- [#231](https://github.com/nf-core/bacass/pull/231) Fix KmerFinder DB and relative paths resolution issues.

‎tests/.nftignore‎

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@@ -23,10 +23,12 @@ trimming/shortreads/json_html/*.fastp.html
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trimming/shortreads/log/*.fastp.log
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trimming/longreads/porechop/*.porechop.log
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Prokka/*/*.{gbk,sqn,log,err}
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Prokka/*/*.{faa,ffn,fna,fsa,gff,tbl,tsv,txt}
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QUAST/report/**
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Unicycler/*.unicycler.log
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DFAST/*/*.{tsv,log,gbk}
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LIFTOFF/*.gff3
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QC_longreads/ToulligQC/**
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QC_longreads/NanoPlot/*
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QC_longreads/NanoPlot/**
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Dragonflye/*
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Medaka/*

‎tests/.nftignore_files_entirely‎

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@@ -4,4 +4,6 @@ busco/busco_downloads/**
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busco/**/busco_sequences/**
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busco/**/hmmer_output/**
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QC_longreads/ToulligQC/**
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QC_longreads/NanoPlot/*.log
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QC_longreads/NanoPlot/**
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Prokka/*/*.{gbk,sqn,log,err}
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Prokka/*/*.{faa,ffn,fna,fsa,gff,tbl,tsv,txt}

‎tests/default.nf.test.snap‎

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@@ -52,31 +52,7 @@
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"Prokka",
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"Prokka/ERR044595/ERR044595.fna",
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"Prokka/ERR044595/ERR044595.fsa",
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"Prokka/ERR044595/ERR044595.gbk",
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"Prokka/ERR044595/ERR044595.gff",
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"Prokka/ERR044595/ERR044595.log",
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"Prokka/ERR044595/ERR044595.sqn",
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"Prokka/ERR044595/ERR044595.tbl",
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"Prokka/ERR044595/ERR044595.tsv",
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"Prokka/ERR044595/ERR044595.txt",
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"Prokka/ERR064912",
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"Prokka/ERR064912/ERR064912.err",
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"Prokka/ERR064912/ERR064912.faa",
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"Prokka/ERR064912/ERR064912.ffn",
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"Prokka/ERR064912/ERR064912.fna",
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"Prokka/ERR064912/ERR064912.fsa",
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"Prokka/ERR064912/ERR064912.gbk",
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"Prokka/ERR064912/ERR064912.gff",
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"Prokka/ERR064912/ERR064912.log",
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"Prokka/ERR064912/ERR064912.sqn",
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"Prokka/ERR064912/ERR064912.tbl",
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"Prokka/ERR064912/ERR064912.tsv",
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"Prokka/ERR064912/ERR064912.txt",
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"QUAST",
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"QUAST/report",
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"QUAST/report/basic_stats",
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"trimming/shortreads/log/ERR064912.fastp.log"
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],
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[
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"ERR044595.faa:md5,302449e0a43d763b27def8e81afa7d4e",
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"ERR044595.ffn:md5,14065366e562f5385332bb06f2d3a9a3",
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"ERR044595.fna:md5,567484c06921e9100d73d90c883b90fc",
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"ERR044595.fsa:md5,a360d101a51b7c62e36f39ccc9beae7d",
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"ERR044595.gff:md5,1bbc1472a3fee1fe9f846f63b74ff403",
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"ERR044595.tbl:md5,4df278383861e92d8bc0fffc0f6e599d",
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"ERR044595.tsv:md5,27d76c140260e8ca353b16fc492ed4d5",
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"ERR044595.txt:md5,49824bb55b6e942cd180478888fa3ea6",
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"ERR064912.faa:md5,50496c00b2d8c6edb788aef62e5ddcce",
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"ERR064912.ffn:md5,b900491ea7e0f8aadc65341f956869ce",
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"ERR064912.fna:md5,d92d528d30458f33d3102311a77bb715",
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"ERR064912.fsa:md5,cb83ba06350fd4bc5fe91987132c9ff2",
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"ERR064912.gff:md5,1c844174604aa1bebb66891aedb4489f",
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"ERR064912.tbl:md5,f31ec628679d74f2248094764ba048f6",
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"ERR064912.tsv:md5,b917f4ec5a1144ed8dccdb3e665ee33d",
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"ERR064912.txt:md5,a0ea358143d22a547f9445095d7fee6d",
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"ERR044595.assembly.gfa.gz:md5,87769d87d717d40198ef9b340e4747ef",
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"ERR044595.scaffolds.fa.gz:md5,7497990c64bc5572a77b3233bf0fa916",
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"ERR064912.assembly.gfa.gz:md5,01faaeca29910ae15e49dd355dda556a",
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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"nextflow": "25.04.7"
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},
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"timestamp": "2025-09-05T11:00:32.895111033"
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"timestamp": "2025-10-09T11:13:04.342123239"
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}
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}

‎tests/hybrid.nf.test.snap‎

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"Medaka/ERR044595_polished_genome.fa",
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"Prokka",
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"Prokka/ERR044595/ERR044595.fna",
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"Prokka/ERR044595/ERR044595.gbk",
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"Prokka/ERR044595/ERR044595.gff",
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"Prokka/ERR044595/ERR044595.sqn",
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"Prokka/ERR044595/ERR044595.tbl",
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"Prokka/ERR044595/ERR044595.tsv",
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"QC_longreads",
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"QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.html",
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"QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html",
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"QC_longreads/NanoPlot/NanoPlot-report.html",
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"QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html",
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"QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html",
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"QC_longreads/NanoPlot/WeightedHistogramReadlength.html",
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"QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.html",
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"QC_longreads/NanoPlot/Yield_By_Length.html",
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],
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"meta": {
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"nextflow": "25.04.6"
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"nextflow": "25.04.7"
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},
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"timestamp": "2025-09-04T14:58:46.145509956"
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"timestamp": "2025-10-09T11:41:03.883183104"
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}
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}

‎tests/hybrid_dragonflye.nf.test.snap‎

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"Medaka/A1403KPN_polished_genome.fa",
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"QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html",
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"nf-test": "0.9.2",
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"nextflow": "25.04.7"
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},
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"timestamp": "2025-09-04T15:19:28.692454414"
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"timestamp": "2025-10-09T12:03:14.500365955"
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‎tests/long.nf.test.snap‎

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"Prokka/TestMe/TestMe.faa",
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"QC_longreads/NanoPlot/NanoPlot-report.html",
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"QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html",
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"QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html",
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"QC_longreads/NanoPlot/WeightedHistogramReadlength.html",
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"QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.html",
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"nextflow": "25.04.7"
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"timestamp": "2025-09-10T17:53:25.783078319"
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"timestamp": "2025-10-09T12:08:30.581025571"
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‎tests/long_dragonflye.nf.test.snap‎

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"timestamp": "2025-09-10T18:10:21.247421763"
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"timestamp": "2025-10-09T12:26:03.536149595"
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‎tests/long_liftoff.nf.test.snap‎

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"trimming/shortreads/log/ERR064912.fastp.log"
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[
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"ERR044595.gff3:md5,7153b7d4d224c20fc2d532171f71c5ea",
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"ERR044595.unmapped.txt:md5,b4c04cfb80263b48c1937e1144c01bb0",
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"ERR064912.gff3:md5,3765a67d0c2b81990b218f56c9dafb51",
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"ERR064912.unmapped.txt:md5,b4c04cfb80263b48c1937e1144c01bb0",
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"ERR044595.assembly.gfa.gz:md5,66fcb08f315b69b3639ab394f4171f58",
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],
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"meta": {
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"nextflow": "25.04.7"
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"timestamp": "2025-09-10T18:22:21.09205384"
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"timestamp": "2025-10-09T13:38:24.024694858"
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‎tests/long_miniasm.nf.test.snap‎

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"Miniasm/TestMe.fasta.gz",
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"Prokka/TestMe/TestMe.faa",
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"QC_longreads",
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"QC_longreads/NanoPlot",
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"QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html",
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"QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html",
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"QUAST",
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"QUAST/report",
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"nf-test": "0.9.2",
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"nextflow": "25.04.7"
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"timestamp": "2025-09-10T18:26:28.989743936"
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"timestamp": "2025-10-09T12:32:56.633589499"
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}
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}

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