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SHAPEIT5_PHASECOMMON Migrate to nf-test #7061

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SHAPEIT5_PHASECOMMON Migrate to nf-test #7061

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645372b
Migrate to nf-test
Nov 22, 2024
70bac9c
Add options stub
Nov 22, 2024
e40c94b
Merge branch 'master' into shapeit5_phasecommon
LouisLeNezet Nov 22, 2024
5ab7b19
Merge branch 'master' into shapeit5_phasecommon
LouisLeNezet Nov 23, 2024
ee8f804
Merge branch 'master' into shapeit5_phasecommon
LouisLeNezet Nov 25, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/shapeit5/phasecommon/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::shapeit5=1.0.0
- bioconda::shapeit5=5.1.1
14 changes: 7 additions & 7 deletions modules/nf-core/shapeit5/phasecommon/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SHAPEIT5_PHASECOMMON {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/shapeit5:1.0.0--h0c8ee15_0':
'biocontainers/shapeit5:1.0.0--h0c8ee15_0'}"
'https://depot.galaxyproject.org/singularity/shapeit5:5.1.1--hb60d31d_0':
'biocontainers/shapeit5:5.1.1--hb60d31d_0'}"

input:
tuple val(meta) , path(input), path(input_index), path(pedigree), val(region)
Expand All @@ -23,7 +23,7 @@ process SHAPEIT5_PHASECOMMON {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "vcf.gz"
def suffix = task.ext.suffix ?: "bcf"

if ("$input" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

Expand Down Expand Up @@ -51,11 +51,11 @@ process SHAPEIT5_PHASECOMMON {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "vcf.gz"
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "bcf"
def create_cmd = suffix.endsWith(".gz") ? "echo '' | gzip >" : "touch"
"""
touch ${prefix}.${suffix}
${create_cmd} ${prefix}.${suffix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
106 changes: 106 additions & 0 deletions modules/nf-core/shapeit5/phasecommon/tests/main.nf.test
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@@ -0,0 +1,106 @@
nextflow_process {

name "Test Process SHAPEIT5_PHASECOMMON"
script "../main.nf"
process "SHAPEIT5_PHASECOMMON"

tag "modules"
tag "modules_nfcore"
tag "shapeit5"
tag "shapeit5/phasecommon"

test("homo sapiens - bcf, [], [], []") {
when {
process {
"""
input[0] = Channel.of([
[ id:'input', single_end:false ], // meta map
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
[],
"chr21"
])

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Suggested change

input[1] = Channel.of([[],[],[]])
input[2] = Channel.of([[],[],[]])
input[3] = Channel.of([[],[]])
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.phased_variant.collect{ meta, vcf -> [meta, file(vcf).name]},
process.out.versions
).match() }
)
}

}

test("homo sapiens - bcf, [], [], map") {
when {
process {
"""
input[0] = Channel.of([
[ id:'input', single_end:false ], // meta map
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
[],
"chr21"
])

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Suggested change

input[1] = Channel.of([[],[],[]])
input[2] = Channel.of([[],[],[]])
input[3] = Channel.of([
[ id:'map', single_end:false ],
file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
])
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.phased_variant.collect{ meta, vcf -> [meta, file(vcf).name]},
process.out.versions
).match() }
)
}

}

test("homo sapiens - bcf, [], [], [] - stub") {
options '-stub'
when {
process {
"""
input[0] = Channel.of([
[ id:'input', single_end:false ], // meta map
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
[],
"chr21"
])

input[1] = Channel.of([[],[],[]])
input[2] = Channel.of([[],[],[]])
input[3] = Channel.of([[],[]])
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

}
79 changes: 79 additions & 0 deletions modules/nf-core/shapeit5/phasecommon/tests/main.nf.test.snap
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@@ -0,0 +1,79 @@
{
"homo sapiens - bcf, [], [], []": {
"content": [
[
[
{
"id": "input",
"single_end": false
},
"input.bcf"
]
],
[
"versions.yml:md5,135745eaa06583f1c0402134626f9082"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-22T17:42:36.937530107"
},
"homo sapiens - bcf, [], [], map": {
"content": [
[
[
{
"id": "input",
"single_end": false
},
"input.bcf"
]
],
[
"versions.yml:md5,135745eaa06583f1c0402134626f9082"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-22T17:43:02.244755417"
},
"homo sapiens - bcf, [], [], [] - stub": {
"content": [
{
"0": [
[
{
"id": "input",
"single_end": false
},
"input.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,135745eaa06583f1c0402134626f9082"
],
"phased_variant": [
[
{
"id": "input",
"single_end": false
},
"input.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,135745eaa06583f1c0402134626f9082"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-22T18:43:12.707870434"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -525,9 +525,6 @@ sgdemux:
shapeit5/ligate:
- modules/nf-core/shapeit5/ligate/**
- tests/modules/nf-core/shapeit5/ligate/**
shapeit5/phasecommon:
- modules/nf-core/shapeit5/phasecommon/**
- tests/modules/nf-core/shapeit5/phasecommon/**
shapeit5/phaserare:
- modules/nf-core/shapeit5/phaserare/**
- tests/modules/nf-core/shapeit5/phaserare/**
Expand Down
40 changes: 0 additions & 40 deletions tests/modules/nf-core/shapeit5/phasecommon/main.nf
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5 changes: 0 additions & 5 deletions tests/modules/nf-core/shapeit5/phasecommon/nextflow.config
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17 changes: 0 additions & 17 deletions tests/modules/nf-core/shapeit5/phasecommon/test.yml
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