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try porting mmseqs/search to nf-test #7231

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try porting mmseqs/search to nf-test #7231

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4381c1b
try porting to nf-test
famosab Dec 17, 2024
603ffd5
remove from pytest
famosab Dec 17, 2024
4812b52
Apply suggestions from code review
famosab Dec 19, 2024
39bf174
fix stub
famosab Dec 19, 2024
f6bdfb0
remove pytest
famosab Dec 19, 2024
b628d0c
Merge branch 'master' into search
famosab Dec 19, 2024
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8 changes: 3 additions & 5 deletions modules/nf-core/mmseqs/search/main.nf
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@

process MMSEQS_SEARCH {
tag "$meta.id"
label 'process_high'
Expand All @@ -13,7 +12,7 @@ process MMSEQS_SEARCH {
tuple val(meta2), path(db_target)

output:
tuple val(meta), path("${prefix}"), emit: db_search
tuple val(meta), path("${prefix}/"), emit: db_search
path "versions.yml" , emit: versions

when:
Expand Down Expand Up @@ -51,8 +50,7 @@ process MMSEQS_SEARCH {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
if ("$db_query" == "${prefix}" || "$db_target" == "${prefix}" ) error "Input and output names of databases are the same, set prefix in module configuration to disambiguate!"
"""
mkdir -p $prefix
Expand All @@ -62,7 +60,7 @@ process MMSEQS_SEARCH {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mmseqs: \$(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: /')
mmseqs: \$(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //')
END_VERSIONS
"""
}
95 changes: 95 additions & 0 deletions modules/nf-core/mmseqs/search/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,95 @@
nextflow_process {

name "Test Process MMSEQS_SEARCH"
script "../main.nf"
process "MMSEQS_SEARCH"

tag "modules"
tag "modules_nfcore"
tag "mmseqs"
tag "mmseqs/search"
tag "mmseqs/createdb"

config "./nextflow.config"

setup {
run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_QUERY") {
script "../../../mmseqs/createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_query', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
]
"""
}
}

run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_TARGET") {
script "../../../mmseqs/createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_target', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
]
"""
}
}
}

test("sarscov2 - test-search") {

when {
params {
module_args = '--remove-tmp-files 1 --search-type 2'
module_prefix = 'test_output_search'
}
process {
"""
input[0] = MMSEQS_CREATEDB_QUERY.out.db
input[1] = MMSEQS_CREATEDB_TARGET.out.db
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}

}

test("sarscov2 - test-search - stub") {

options "-stub"

when {
params {
module_args = '--remove-tmp-files 1 --search-type 2'
module_prefix = 'test_output_search'
}
process {
"""
input[0] = MMSEQS_CREATEDB_QUERY.out.db
input[1] = MMSEQS_CREATEDB_TARGET.out.db
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}

}

}
68 changes: 68 additions & 0 deletions modules/nf-core/mmseqs/search/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,68 @@
{
"sarscov2 - test-search - stub": {
"content": [
{
"0": [
[
{
"id": "test_query",
"single_end": true
},
[
"test_output_search.0:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.1:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.2:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.3:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.4:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.5:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.6:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.7:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.8:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.9:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.index:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
"versions.yml:md5,186c905c6a33d4175414a55ffb169711"
],
"db_search": [
[
{
"id": "test_query",
"single_end": true
},
[
"test_output_search.0:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.1:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.2:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.3:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.4:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.5:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.6:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.7:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.8:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.9:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
"test_output_search.index:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,186c905c6a33d4175414a55ffb169711"
]
},
{
"MMSEQS_SEARCH": {
"mmseqs": 1.47E+285
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-19T13:58:05.087961"
}
}
8 changes: 8 additions & 0 deletions modules/nf-core/mmseqs/search/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
process {

withName: MMSEQS_SEARCH {
ext.prefix = params.module_prefix
ext.args = params.module_args
}

}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -347,9 +347,6 @@ mitohifi/mitohifi:
mmseqs/easysearch:
- modules/nf-core/mmseqs/easysearch/**
- tests/modules/nf-core/mmseqs/easysearch/**
mmseqs/search:
- modules/nf-core/mmseqs/search/**
- tests/modules/nf-core/mmseqs/search/**
mmseqs/tsv2exprofiledb:
- modules/nf-core/mmseqs/tsv2exprofiledb/**
- tests/modules/nf-core/mmseqs/tsv2exprofiledb/**
Expand Down
23 changes: 0 additions & 23 deletions tests/modules/nf-core/mmseqs/search/main.nf
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17 changes: 0 additions & 17 deletions tests/modules/nf-core/mmseqs/search/nextflow.config
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11 changes: 0 additions & 11 deletions tests/modules/nf-core/mmseqs/search/test.yml
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