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Merge branch 'master' into dbsnp
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@famosab
famosab authored Dec 11, 2024
2 parents 0d3a149 + a62c798 commit 52962d5
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Showing 11 changed files with 240 additions and 129 deletions.
2 changes: 2 additions & 0 deletions .github/conda_skip.yml
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Expand Up @@ -184,5 +184,7 @@ exclude:
path: modules/nf-core/xeniumranger/import-segmentation
- profile: conda
path: modules/nf-core/parabricks/dbsnp
- profile: conda
path: modules/nf-core/parabricks/indexgvcf
- profile: conda
path: modules/nf-core/parabricks/genotypegvcf
28 changes: 10 additions & 18 deletions modules/nf-core/parabricks/indexgvcf/main.nf
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@@ -1,16 +1,17 @@
process PARABRICKS_INDEXGVCF {
tag "$meta.id"
label 'process_high'
label 'process_gpu'
stageInMode 'copy' // needed by the module to work properly - might be removed when this is fixed upstream

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("*.{idx,tbi}") , emit: gvcf_index
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -21,12 +22,12 @@ process PARABRICKS_INDEXGVCF {
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 num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
"""
pbrun \\
indexgvcf \\
--input $gvcf \\
$num_gpus \\
$args
cat <<-END_VERSIONS > versions.yml
Expand All @@ -39,19 +40,10 @@ process PARABRICKS_INDEXGVCF {
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

def output_cmd = gvcf.any{ it.name.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}":
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8 changes: 5 additions & 3 deletions modules/nf-core/parabricks/indexgvcf/meta.yml
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Expand Up @@ -30,9 +30,11 @@ output:
type: map
description: |
Groovy Map containing output information
- "*.g.vcf*":
type: file
description: Indexed gvcf file
pattern: "*.g.vcf"
- "*.{idx,tbi}":
type: map
description: |
Groovy Map containing output information
pattern: "*.g.vcf"
- versions:
- versions.yml:
Expand Down
109 changes: 109 additions & 0 deletions modules/nf-core/parabricks/indexgvcf/tests/main.nf.test
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@@ -0,0 +1,109 @@
nextflow_process {

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

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

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(
file(process.out.gvcf_index[0][1]).name,
process.out.versions
).match()
}
)
}

}

test("human - gvcf.gz") {

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
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(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() }
)
}

}

}
114 changes: 114 additions & 0 deletions modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap
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@@ -0,0 +1,114 @@
{
"human - gvcf.gz": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec"
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
"test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec"
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-10T10:16:48.994612337"
},
"human - gvcf": {
"content": [
"test.genome.g.vcf.idx",
[
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-10T10:21:20.010561875"
},
"human - gvcf - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
"test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-10T10:21:32.292223281"
},
"human - gvcf.gz - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
"gvcf_index": [
[
{
"id": "test"
},
"test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-10T10:14:58.744532337"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -398,9 +398,6 @@ parabricks/deepvariant:
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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5 changes: 0 additions & 5 deletions tests/modules/nf-core/parabricks/indexgvcf/nextflow.config
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19 changes: 0 additions & 19 deletions tests/modules/nf-core/parabricks/indexgvcf/test.yml
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