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port parabricks/indexgvcf to nf-test #6996

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port parabricks/indexgvcf to nf-test #6996

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c1ad6e9
port parabricks/indexgvcf to nf-test
famosab Nov 14, 2024
1db22b2
Merge branch 'master' into indexg
mashehu Nov 16, 2024
973bb35
Merge branch 'master' into indexg
famosab Nov 18, 2024
8ad72fd
update test yaml
famosab Nov 18, 2024
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3 changes: 3 additions & 0 deletions .github/workflows/test.yml
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Expand Up @@ -662,6 +662,7 @@ jobs:
- path: modules/nf-core/parabricks/fq2bammeth
- path: modules/nf-core/parabricks/fq2bam
- path: modules/nf-core/parabricks/applybqsr
- path: modules/nf-core/parabricks/indexgvcf
- profile: conda
path: modules/nf-core/xeniumranger/relabel
- profile: conda
Expand Down Expand Up @@ -698,6 +699,8 @@ jobs:
profile: [docker_self_hosted, singularity]
- path: modules/nf-core/parabricks/fq2bammeth
profile: [docker_self_hosted, singularity]
- path: modules/nf-core/parabricks/indexgvcf
profile: [docker_self_hosted, singularity]
env:
NXF_ANSI_LOG: false

Expand Down
25 changes: 9 additions & 16 deletions modules/nf-core/parabricks/indexgvcf/main.nf
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Original file line number Diff line number Diff line change
@@ -1,16 +1,17 @@
process PARABRICKS_INDEXGVCF {
tag "$meta.id"
label 'process_high'
label 'process_gpu'

container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1"

input:
tuple val(meta), path(gvcf, stageAs:'')
tuple val(meta), path(gvcf)

output:
// This tool outputs g.vcf.idx if input is uncompressed, g.vcf.gz.tbi if input is compressed
tuple val(meta), path("*.g.vcf*") , emit: gvcf_index
path "versions.yml" , emit: versions
tuple val(meta), path("*") , emit: gvcf_index
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -22,11 +23,12 @@ process PARABRICKS_INDEXGVCF {
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
"""
pbrun \\
indexgvcf \\
--input $gvcf \\
$num_gpus \\
$args

cat <<-END_VERSIONS > versions.yml
Expand All @@ -39,19 +41,10 @@ process PARABRICKS_INDEXGVCF {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

def output_cmd = gvcf.collect{ it.getExtension().endsWith("gz") } ? "touch ${prefix}.g.vcf.gz.tbi" : "touch ${prefix}.g.vcf.idx"
"""
# Different outputs generated depending if file is gzipped
case $gvcf in
*.gz )
touch ${prefix}.g.vcf.gz.tbi
;;
* )
touch ${prefix}.g.vcf.idx
;;
esac
$output_cmd

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

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

tag "modules"
tag "modules_nfcore"
tag "parabricks"
tag "parabricks/indexgvcf"

test("human - gvcf") {

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
]
"""
}
}

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

}

test("human - gvcf.gz") {

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/0f9d382fb977a63114e2ae3d59a320dbedba0311/data/genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz')
//file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true)
]
"""
}
}

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

}

test("human - gvcf - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
]
"""
}
}

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

}

test("human - gvcf.gz - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/0f9d382fb977a63114e2ae3d59a320dbedba0311/data/genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz')
//file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true)
]
"""
}
}

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

}

}
148 changes: 148 additions & 0 deletions modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap
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@@ -0,0 +1,148 @@
{
"human - gvcf.gz": {
"content": [
{
"0": [
[
{
"id": "test"
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
},
"versions.yml"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T16:09:18.936863233"
},
"human - gvcf": {
"content": [
{
"0": [
[
{
"id": "test"
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T16:11:41.309055746"
},
"human - gvcf - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
[
"test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T16:07:41.345829979"
},
"human - gvcf.gz - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
[
"test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T16:07:47.461957869"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -461,9 +461,6 @@ parabricks/genotypegvcf:
parabricks/haplotypecaller:
- modules/nf-core/parabricks/haplotypecaller/**
- tests/modules/nf-core/parabricks/haplotypecaller/**
parabricks/indexgvcf:
- modules/nf-core/parabricks/indexgvcf/**
- tests/modules/nf-core/parabricks/indexgvcf/**
parabricks/mutectcaller:
- modules/nf-core/parabricks/mutectcaller/**
- tests/modules/nf-core/parabricks/mutectcaller/**
Expand Down
53 changes: 0 additions & 53 deletions tests/modules/nf-core/parabricks/indexgvcf/main.nf
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