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port parabricks/indexgvcf to nf-test #6996

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merged 22 commits into from
Dec 11, 2024
Merged

port parabricks/indexgvcf to nf-test #6996

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4c6e3ba
port parabricks/indexgvcf to nf-test
famosab Nov 14, 2024
f86ee86
fix linting
famosab Nov 21, 2024
e2a47a0
update test yaml
famosab Nov 18, 2024
65243bb
remove test.yml
famosab Nov 21, 2024
236f271
remove log
famosab Nov 21, 2024
917961b
Merge branch 'master' into indexg
famosab Nov 25, 2024
2eb3452
add to conda_skip
famosab Dec 2, 2024
885711c
Merge branch 'master' into indexg
famosab Dec 2, 2024
b87aab8
add tag gpu
famosab Dec 2, 2024
774a6e0
try different profile combination
mashehu Dec 3, 2024
a1ff3d0
avoid string concatination
mashehu Dec 3, 2024
7aba8a8
revert changes to profile
mashehu Dec 3, 2024
af77e8d
Merge branch 'master' into indexg
famosab Dec 9, 2024
09a76ec
update snap - sorry
famosab Dec 9, 2024
b996539
Merge branch 'indexg' of github.com:famosab/modules into indexg
famosab Dec 9, 2024
2144582
Merge branch 'master' into indexg
famosab Dec 10, 2024
b459ca5
fix: testfile paths
famosab Dec 10, 2024
92943f0
fix: index file is now created
famosab Dec 10, 2024
8866688
fix linting
famosab Dec 10, 2024
d4c8c71
Merge branch 'master' into indexg
famosab Dec 10, 2024
f28a84e
Update modules/nf-core/parabricks/indexgvcf/main.nf
famosab Dec 11, 2024
5ebb378
Merge branch 'master' into indexg
famosab Dec 11, 2024
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2 changes: 2 additions & 0 deletions .github/conda_skip.yml
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Expand Up @@ -182,3 +182,5 @@ exclude:
path: modules/nf-core/xeniumranger/resegment
- profile: conda
path: modules/nf-core/xeniumranger/import-segmentation
- profile: conda
path: modules/nf-core/parabricks/indexgvcf
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
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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
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"
- "*":
type: map
description: |
Groovy Map containing output information
pattern: "*.g.vcf"
- versions:
- versions.yml:
Expand Down
107 changes: 107 additions & 0 deletions modules/nf-core/parabricks/indexgvcf/tests/main.nf.test
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@@ -0,0 +1,107 @@
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(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)
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]
"""
}
}

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)
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]
"""
}
}

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

}

}
146 changes: 146 additions & 0 deletions modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,146 @@
{
"human - gvcf.gz": {
"content": [
{
"0": [
[
{
"id": "test"
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"1": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
],
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"gvcf_index": [
[
{
"id": "test"
},
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
],
"versions": [
"versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-09T15:26:59.639869164"
},
"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"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-09T15:26:53.046037224"
},
"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 @@ -407,9 +407,6 @@ 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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