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port parabricks/deepvariant to nf-test #6995

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port parabricks/deepvariant to nf-test #6995

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d38760a
port to nf-test
famosab Nov 14, 2024
94d726f
remove
famosab Nov 14, 2024
3acb809
update test yaml
famosab Nov 18, 2024
f87d2d9
swap to nextflow config
famosab Nov 21, 2024
32e24fa
finalize
famosab Nov 21, 2024
3f7444d
revert changes to nf-test config
famosab Nov 22, 2024
220f99d
revert changes to nf-test config
famosab Nov 22, 2024
35eab5d
add to conda_skip
famosab Dec 2, 2024
45fc76f
Merge branch 'master' into deepv
famosab Dec 2, 2024
053c1d3
add tag gpu
famosab Dec 2, 2024
894bb4a
Merge branch 'master' into deepv
famosab Dec 9, 2024
3c4aa44
Merge branch 'master' into deepv
famosab Dec 10, 2024
13420bb
Update modules/nf-core/parabricks/deepvariant/tests/nextflow.config
famosab Dec 11, 2024
dc18210
Update modules/nf-core/parabricks/deepvariant/main.nf
famosab Dec 11, 2024
1d64fdf
Merge branch 'master' into deepv
famosab Dec 11, 2024
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2 changes: 2 additions & 0 deletions .github/conda_skip.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -182,6 +182,8 @@ exclude:
path: modules/nf-core/xeniumranger/resegment
- profile: conda
path: modules/nf-core/xeniumranger/import-segmentation
- profile: conda
path: modules/nf-core/parabricks/deepvariant
- profile: conda
path: modules/nf-core/parabricks/dbsnp
- profile: conda
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15 changes: 7 additions & 8 deletions modules/nf-core/parabricks/deepvariant/main.nf
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
process PARABRICKS_DEEPVARIANT {
tag "$meta.id"
label 'process_high'
label 'process_gpu'
stageInMode 'copy' // needed by the module to work properly can be removed when 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(input), path(input_index), path(interval_file)
Expand All @@ -16,25 +18,23 @@ process PARABRICKS_DEEPVARIANT {
task.ext.when == null || task.ext.when

script:

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
}

def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def output_file = args =~ "gvcf" ? "${prefix}.g.vcf" : "${prefix}.vcf"
def output_file = ("--gvcf" =~ task.ext.args)? "${prefix}.g.vcf" : "${prefix}.vcf"
def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
"""

pbrun \\
deepvariant \\
--ref $fasta \\
--in-bam $input \\
--out-variants $output_file \\
$interval_file_command \\
--num-gpus $task.accelerator.request \\
$num_gpus \\
$args

cat <<-END_VERSIONS > versions.yml
Expand All @@ -44,9 +44,8 @@ process PARABRICKS_DEEPVARIANT {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def output_file = args =~ "gvcf" ? "${prefix}.g.vcf" : "${prefix}.vcf"
def output_file = ("--gvcf" =~ task.ext.args)? "${prefix}.g.vcf" : "${prefix}.vcf"
"""
touch $output_file

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178 changes: 178 additions & 0 deletions modules/nf-core/parabricks/deepvariant/tests/main.nf.test
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@@ -0,0 +1,178 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "parabricks"
tag "parabricks/deepvariant"
tag "gpu"

test("human - bam") {

when {
process {
"""
input[0] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
[], // bam.bai not needed unless using intervals
[]
]
input[1] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
path(process.out.vcf[0][1]).vcf.variantsMD5,
process.out.versions
).match() }
)
}

}

test("human - bam - intervals") {

config './nextflow.config'

when {
process {
"""
input[0] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
]
input[1] = [
[ id:'ref'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
path(process.out.vcf[0][1]).vcf.variantsMD5,
process.out.versions
).match() }
)
}

}

test("human - bam - intervals - gvcf") {

config './nextflow.config'

when {
params {
module_args = '--gvcf'
}
process {
"""
input[0] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
]
input[1] = [
[ id:'ref'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.versions,
// file(process.out.vcf[0][1]).name // fails with groovy.lang.MissingMethodException: No signature of method: static com.askimed.nf.test.lang.extensions.GlobalMethods.file() is applicable for argument types: (ArrayList) values:
).match()
}
)
}

}

test("human - bam - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
[], // bam.bai not needed unless using intervals
[]
]
input[1] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
}

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

}

test("human - bam - intervals - gvcf - stub") {

config './nextflow.config'
options "-stub"

when {
params {
module_args = '--gvcf'
}
process {
"""
input[0] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
]
input[1] = [
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
}

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

}

}
106 changes: 106 additions & 0 deletions modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
{
"human - bam - intervals - gvcf": {
"content": [
[
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T15:26:48.481295634"
},
"human - bam - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
],
"vcf": [
[
{
"id": "test"
},
"test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T15:05:28.449273519"
},
"human - bam - intervals": {
"content": [
"27097afc7aae62918a3e26790cc189c3",
[
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T15:06:52.854870182"
},
"human - bam": {
"content": [
"8b526a232f93a5036176336415abf7d1",
[
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T15:06:37.651354312"
},
"human - bam - intervals - gvcf - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.g.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
],
"vcf": [
[
{
"id": "test"
},
"test.g.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-14T15:12:11.438654866"
}
}
7 changes: 7 additions & 0 deletions modules/nf-core/parabricks/deepvariant/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
process {

withName: 'PARABRICKS_DEEPVARIANT' {
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 @@ -392,9 +392,6 @@ ncbitools/vecscreen:
oncocnv:
- modules/nf-core/oncocnv/**
- tests/modules/nf-core/oncocnv/**
parabricks/deepvariant:
- modules/nf-core/parabricks/deepvariant/**
- tests/modules/nf-core/parabricks/deepvariant/**
parabricks/haplotypecaller:
- modules/nf-core/parabricks/haplotypecaller/**
- tests/modules/nf-core/parabricks/haplotypecaller/**
Expand Down
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