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Merged
SPPearce merged 3 commits into from
Apr 11, 2025
Merged

Migrate genmap/map to nf-test #8279

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fb7e223
Migrate to nf-test
Apr 11, 2025
4ef4bf8
Merge branch 'master' into genmap
LouisLeNezet Apr 11, 2025
0e9cba4
Update prefix
Apr 11, 2025
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18 changes: 9 additions & 9 deletions modules/nf-core/genmap/map/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,9 @@ process GENMAP_MAP {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "$meta.id"
def bed = regions ? "--selection ${regions}" : ""
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}_map"
def bed = regions ? "--selection ${regions}" : ""

if ("$index" == "${prefix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
Expand All @@ -43,13 +43,13 @@ process GENMAP_MAP {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "$meta.id"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}_map"
def token_args = args.tokenize(" ")
def wig = token_args.contains("-w") || token_args.contains("--wig") ? "touch ${prefix}.wig" : ""
def bg = token_args.contains("-bg") || token_args.contains("--bedgraph") ? "touch ${prefix}.bedgraph" : ""
def txt = token_args.contains("-t") || token_args.contains("--txt") ? "touch ${prefix}.txt" : ""
def csv = token_args.contains("-d") || token_args.contains("--csv") ? "touch ${prefix}.csv" : ""
def wig = token_args.contains("-w") || token_args.contains("--wig") ? "touch ${prefix}.wig" : ""
def bg = token_args.contains("-bg") || token_args.contains("--bedgraph") ? "touch ${prefix}.bedgraph" : ""
def txt = token_args.contains("-t") || token_args.contains("--txt") ? "touch ${prefix}.txt" : ""
def csv = token_args.contains("-d") || token_args.contains("--csv") ? "touch ${prefix}.csv" : ""

if ("$index" == "${prefix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
Expand Down
79 changes: 79 additions & 0 deletions modules/nf-core/genmap/map/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,79 @@
nextflow_process {

name "Test Process GENMAP_MAP"
config "./nextflow.config"
script "../main.nf"
process "GENMAP_MAP"

tag "modules"
tag "modules_nfcore"
tag "genmap"
tag "genmap/index"
tag "genmap/map"

setup {
run("GENMAP_INDEX") {
script "../../index/main.nf"
process {
"""
input[0] = [
[id:"test"],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true)
]
"""
}
}
}

test("sarscov2 - index bed") {

when {
params {
module_args = "-K 50 -E 2 -w -t -bg -d"
}
process {
"""
input[0] = GENMAP_INDEX.out.index.view()
input[1] = [
[id:"bed"],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}


test("sarscov2 - index bed -- stub") {
options '-stub'
when {
params {
module_args = "-K 50 -E 2 -w -t -bg -d"
}
process {
"""
input[0] = GENMAP_INDEX.out.index
input[1] = [
[id:"bed"],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}
}
}
169 changes: 169 additions & 0 deletions modules/nf-core/genmap/map/tests/main.nf.test.snap
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@@ -0,0 +1,169 @@
{
"sarscov2 - index bed": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_map.wig:md5,c940a5c35af6ac1c11ecc87b7662fc2a"
]
],
"1": [
[
{
"id": "test"
},
"test_map.bedgraph:md5,27ca54c920f3ff0c5985384e557a40f2"
]
],
"2": [
[
{
"id": "test"
},
"test_map.txt:md5,7f9aeaa3d174bb5e6f552efd4f857b4e"
]
],
"3": [
[
{
"id": "test"
},
"test_map.csv:md5,4167a6c7ffbecc1a239c5c1e16b2cbc5"
]
],
"4": [
"versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
],
"bedgraph": [
[
{
"id": "test"
},
"test_map.bedgraph:md5,27ca54c920f3ff0c5985384e557a40f2"
]
],
"csv": [
[
{
"id": "test"
},
"test_map.csv:md5,4167a6c7ffbecc1a239c5c1e16b2cbc5"
]
],
"txt": [
[
{
"id": "test"
},
"test_map.txt:md5,7f9aeaa3d174bb5e6f552efd4f857b4e"
]
],
"versions": [
"versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
],
"wig": [
[
{
"id": "test"
},
"test_map.wig:md5,c940a5c35af6ac1c11ecc87b7662fc2a"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-04-11T16:10:45.401177409"
},
"sarscov2 - index bed -- stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_map.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test"
},
"test_map.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test"
},
"test_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
[
{
"id": "test"
},
"test_map.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
"versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
],
"bedgraph": [
[
{
"id": "test"
},
"test_map.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"csv": [
[
{
"id": "test"
},
"test_map.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"txt": [
[
{
"id": "test"
},
"test_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,c510ddb0e56c8961d4cf9d538a789087"
],
"wig": [
[
{
"id": "test"
},
"test_map.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
},
{
"GENMAP_MAP": {
"genmap": "1.3.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-04-11T16:10:51.374175856"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/genmap/map/tests/nextflow.config
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@@ -0,0 +1,5 @@
process {
withName: "GENMAP_MAP" {
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 @@ -21,9 +21,6 @@ gangstr:
gatk/indelrealigner:
- modules/nf-core/gatk/indelrealigner/**
- tests/modules/nf-core/gatk/indelrealigner/**
genmap/map:
- modules/nf-core/genmap/map/**
- tests/modules/nf-core/genmap/map/**
gget/gget:
- modules/nf-core/gget/gget/**
- tests/modules/nf-core/gget/gget/**
Expand Down
22 changes: 0 additions & 22 deletions tests/modules/nf-core/genmap/map/main.nf
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14 changes: 0 additions & 14 deletions tests/modules/nf-core/genmap/map/nextflow.config
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15 changes: 0 additions & 15 deletions tests/modules/nf-core/genmap/map/test.yml
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