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Delete test files from the repo and use nf-core datasets instead #71

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Merged
ochkalova merged 3 commits into from
Jun 10, 2026
Merged

Delete test files from the repo and use nf-core datasets instead #71

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ec11e17
remove study metadata files
ochkalova Jun 10, 2026
12769af
remove test files for COUNT_RNA module
ochkalova Jun 10, 2026
79174bb
replace test files for RENAME_FASTA_FOR_CATPACK module and update sna…
ochkalova Jun 10, 2026
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6 changes: 0 additions & 6 deletions assets/study_metadata.json
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2 changes: 0 additions & 2 deletions assets/study_metadata.tsv
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2 changes: 1 addition & 1 deletion conf/test_assembly_no_study_complete_metadata.config
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Expand Up @@ -27,7 +27,7 @@ params {

mode = "metagenomic_assemblies"
submission_study = null
study_metadata = "$projectDir/assets/study_metadata.json"
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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2 changes: 1 addition & 1 deletion conf/test_mag_no_study_complete_metadata.config
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Expand Up @@ -27,7 +27,7 @@ params {

mode = "mags"
submission_study = null
study_metadata = "$projectDir/assets/study_metadata.json"
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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2 changes: 0 additions & 2 deletions docs/usage.md
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Expand Up @@ -198,8 +198,6 @@ study-soil-2026 Soil microbiome study Survey of soil microbiota
| `existing_study_type` | No | ENA study type (e.g. `Metagenomics`, `Other`). |
| `new_study_type` | No | Custom study type. Only used when `existing_study_type` is set to `Other`. |

An example metadata file is available at [assets/study_metadata.json](../assets/study_metadata.json).

@ochkalova ochkalova Jun 10, 2026

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There is an example above in the doc anyway, so I think it's fine to just remove this line


## Database preparation (`mags` / `bins`)

The `GENOMESUBMIT` workflow uses `CheckM2` and `CAT_pack` that require specialized databases for completeness/contamination assessment and taxonomy assignment.
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84 changes: 0 additions & 84 deletions modules/local/count_rna/tests/data/ecoli.stats
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23 changes: 0 additions & 23 deletions modules/local/count_rna/tests/data/ecoli_bac.gff
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8 changes: 4 additions & 4 deletions modules/local/count_rna/tests/main.nf.test
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Expand Up @@ -13,8 +13,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file("$moduleDir/tests/data/ecoli.stats", checkIfExists: true),
file("$moduleDir/tests/data/ecoli_bac.gff", checkIfExists: true)
file(params.pipelines_testdata_base_path + 'test_data/rna_search/ecoli.stats', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'test_data/rna_search/ecoli_bac.gff', checkIfExists: true)
]
input[1] = 18
input[2] = 80
Expand Down Expand Up @@ -48,8 +48,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file("$moduleDir/tests/data/ecoli.stats", checkIfExists: true),
file("$moduleDir/tests/data/ecoli_bac.gff", checkIfExists: true)
file(params.pipelines_testdata_base_path + 'test_data/rna_search/ecoli.stats', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'test_data/rna_search/ecoli_bac.gff', checkIfExists: true)
]
input[1] = 18
input[2] = 80
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6 changes: 3 additions & 3 deletions modules/local/registerstudy/tests/main.nf.test
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Expand Up @@ -14,7 +14,7 @@ nextflow_process {
"""
input[0] = [
[ id:'example_study' ],
file("$projectDir/assets/study_metadata.json", checkIfExists: true)
file(params.pipelines_testdata_base_path + 'test_data/study_metadata/study_metadata.json', checkIfExists: true)
]
input[1] = true
"""
Expand All @@ -38,7 +38,7 @@ nextflow_process {
"""
input[0] = [
[ id:'example_study_tsv' ],
file("$projectDir/assets/study_metadata.tsv", checkIfExists: true)
file(params.pipelines_testdata_base_path + 'test_data/study_metadata/study_metadata.tsv', checkIfExists: true)
]
input[1] = true
"""
Expand All @@ -63,7 +63,7 @@ nextflow_process {
"""
input[0] = [
[ id:'example_study' ],
file("$projectDir/assets/study_metadata.json", checkIfExists: true)
file(params.pipelines_testdata_base_path + 'test_data/study_metadata/study_metadata.json', checkIfExists: true)
]
input[1] = true
"""
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4 changes: 2 additions & 2 deletions modules/local/rename_fasta_for_catpack/tests/main.nf.test
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Expand Up @@ -14,7 +14,7 @@ nextflow_process {
"""
input[0] = [
[ id: 'test' ],
file("${moduleDir}/tests/test.fasta", checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true)
]
"""
}
Expand All @@ -38,7 +38,7 @@ nextflow_process {
"""
input[0] = [
[ id: 'test_compressed' ],
file("${moduleDir}/tests/test_compressed.fa.gz", checkIfExists: true)
file(params.pipelines_testdata_base_path + 'test_data/bins/ecoli.fna.gz', checkIfExists: true)
]
"""
}
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24 changes: 12 additions & 12 deletions modules/local/rename_fasta_for_catpack/tests/main.nf.test.snap
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Expand Up @@ -7,24 +7,24 @@
{
"id": "test"
},
"test.fasta:md5,3dc842bfe6f1059ccb006fc454437ebf"
"sarscov2.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
]
],
"renamed_fasta": [
[
{
"id": "test"
},
"test.fasta:md5,3dc842bfe6f1059ccb006fc454437ebf"
"sarscov2.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
]
]
}
],
"timestamp": "2026-06-10T11:55:03.914764",
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.1"
},
"timestamp": "2026-03-25T16:51:01.874131"
"nf-test": "0.9.5",
"nextflow": "26.04.1"
}
},
"RENAME_FASTA_FOR_CATPACK - compressed fasta": {
"content": [
Expand All @@ -34,23 +34,23 @@
{
"id": "test_compressed"
},
"test_compressed.fasta:md5,b349eb81b2fc8db6a6cee870c8d4b054"
"ecoli.fasta:md5,f958ab9c196608148e2863d87d64e28a"
]
],
"renamed_fasta": [
[
{
"id": "test_compressed"
},
"test_compressed.fasta:md5,b349eb81b2fc8db6a6cee870c8d4b054"
"ecoli.fasta:md5,f958ab9c196608148e2863d87d64e28a"
]
]
}
],
"timestamp": "2026-06-10T11:55:08.127169",
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.1"
},
"timestamp": "2026-03-25T16:51:04.916201"
"nf-test": "0.9.5",
"nextflow": "26.04.1"
}
}
}
4 changes: 0 additions & 4 deletions modules/local/rename_fasta_for_catpack/tests/test.fasta
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