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port parabricks/mutectcaller to nf-test #6991

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port parabricks/mutectcaller to nf-test #6991

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192699b
port to nf-test
famosab Nov 13, 2024
fca1546
change conf
famosab Nov 13, 2024
fdd5ce6
add num_gpu
famosab Nov 13, 2024
5fe3310
comment out some tests
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409a86e
comment out some tests
famosab Nov 13, 2024
3613eec
only stub
famosab Nov 13, 2024
9cf060a
only stub
famosab Nov 13, 2024
a56692a
stub snap works
famosab Nov 13, 2024
ae10a6b
add normal test
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52cf9bf
low mem
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971c2a9
add more tests
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wip
famosab Nov 14, 2024
d240c88
add working tests
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d48fee6
update test
famosab Nov 15, 2024
1acf6ac
Merge branch 'master' into mutectcaller
famosab Nov 18, 2024
511280a
update test yaml
famosab Nov 18, 2024
413da91
port to nf-test
famosab Nov 13, 2024
47c8910
change conf
famosab Nov 13, 2024
d7f5501
add num_gpu
famosab Nov 13, 2024
16d1f20
comment out some tests
famosab Nov 13, 2024
d738f10
comment out some tests
famosab Nov 13, 2024
0a70e99
only stub
famosab Nov 13, 2024
7937399
only stub
famosab Nov 13, 2024
2845150
stub snap works
famosab Nov 13, 2024
4661874
add normal test
famosab Nov 13, 2024
d404aa9
low mem
famosab Nov 13, 2024
bc93c65
add more tests
famosab Nov 13, 2024
acf65af
wip
famosab Nov 14, 2024
a2faa76
add working tests
famosab Nov 14, 2024
8b6eced
update test
famosab Nov 15, 2024
0f32b3c
swap to one config
famosab Nov 21, 2024
6411112
add to conda_skip
famosab Dec 2, 2024
2b01c09
Merge branch 'master' into mutectcaller
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99eee96
add tag gpu
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af856b8
Merge branch 'master' into mutectcaller
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8a96f48
update snap
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Merge branch 'master' into mutectcaller
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Apply suggestions from code review
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Merge branch 'master' into mutectcaller
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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 @@ -183,4 +183,6 @@ exclude:
- profile: conda
path: modules/nf-core/xeniumranger/import-segmentation
- profile: conda
path: modules/nf-core/parabricks/mutectcaller
- profile: conda
path: modules/nf-core/parabricks/genotypegvcf
10 changes: 6 additions & 4 deletions modules/nf-core/parabricks/mutectcaller/main.nf
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
process PARABRICKS_MUTECTCALLER {
tag "$meta.id"
label 'process_high'
label 'process_gpu'

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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(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(interval_file)
Expand Down Expand Up @@ -30,6 +31,7 @@ process PARABRICKS_MUTECTCALLER {
def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
def prepon_command = panel_of_normals ? "cp -L $panel_of_normals_index `readlink -f $panel_of_normals`.tbi && pbrun prepon --in-pon-file $panel_of_normals" : ""
def postpon_command = panel_of_normals ? "pbrun postpon --in-vcf ${prefix}.vcf.gz --in-pon-file $panel_of_normals --out-vcf ${prefix}_annotated.vcf.gz" : ""
def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ""
"""

# if panel of normals specified, run prepon
Expand All @@ -42,7 +44,7 @@ process PARABRICKS_MUTECTCALLER {
--tumor-name ${meta.tumor_id} \\
--out-vcf ${prefix}.vcf.gz \\
$interval_file_command \\
--num-gpus $task.accelerator.request \\
$num_gpus \\
$args

# if panel of normals specified, run postpon
Expand All @@ -57,9 +59,9 @@ process PARABRICKS_MUTECTCALLER {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def postpon_command = panel_of_normals ? "touch ${prefix}_annotated.vcf.gz" : ""
def postpon_command = panel_of_normals ? "echo '' | gzip > ${prefix}_annotated.vcf.gz" : ""
"""
touch ${prefix}.vcf.gz
echo "" | gzip > ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.stats
$postpon_command

Expand Down
297 changes: 297 additions & 0 deletions modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
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@@ -0,0 +1,297 @@
nextflow_process {

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

tag "modules"
tag "parabricks/mutectcaller"
tag "modules_nfcore"
tag "parabricks"
tag "gpu"

test("human - bam") {

config "./nextflow.config"

when {
params {
module_args = "--mutect-low-memory"
}
process {
"""
input[0] = [
[ id:'test', tumor_id:'tumour' ],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
[], // index only neeeded if using intervals or tumor-normal calling
[],
[],
[]
]
input[1] = [ // fasta
[ id: 'reference' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
]
input[2] = [] // pon
input[3] = [] // pon index
"""
}
}

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

}

// test("human - bam - tn") {
// // tumor-normal calling not passing because of issue with readgroups in the test files
// // [PB Error][src/readers.cpp:1314] ID simulation01 maps to tm_simulation01, but PU is nm_simulation01 (different platform), exiting.

// config "./nextflow.config"

// when {
// params {
// module_args = "--in-normal-bam $normal_bam --normal-name $meta.normal_id --mutect-low-memory"
// }
// process {
// """
// input[0] = [
// [ id:'test', tumor_id:'tumour', normal_id:'normal' ],
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
// []
// ]
// input[1] = [ // fasta
// [ id: 'reference' ], //genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
// // file()
// file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
// ]
// input[2] = [] // pon
// input[3] = [] // pon index
// """
// }
// }

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

// }

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

// config "./nextflow.config"

// when {
// params {
// module_args = "--mutect-low-memory"
// }
// process {
// """
// input[0] = [
// [ id:'test', tumor_id:'tumor' ],
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
// [],
// [],
// file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
// ]
// input[1] = [ // fasta
// [ id: 'reference' ],
// file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
// ]
// input[2] = [] // pon
// input[3] = [] // pon index
// """
// }
// }

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

// }

// test("human - bam - tn - intervals") {
// // tumor-normal calling not passing because of issue with readgroups in the test files
// // [PB Error][src/readers.cpp:1314] ID simulation01 maps to tm_simulation01, but PU is nm_simulation01 (different platform), exiting.

// config "./nextflow.config"

// when {
// params {
// module_args = "--in-normal-bam $normal_bam --normal-name $meta.normal_id --mutect-low-memory"
// }
// process {
// """
// input[0] = [
// [ id:'test', tumor_id:'tumor', normal_id:'normal'],
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
// ]
// input[1] = [ // fasta
// [ id: 'reference' ],
// file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
// ]
// input[2] = [] // pon
// input[3] = [] // pon index
// """
// }
// }

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

// }

// test("human - bam - pon") {
// // PON test not passing because the tool expects all chromosomes in the PON file to
// // be present in the reference genome.

// config "./nextflow.config"

// when {
// params {
// module_args = "--pon $panel_of_normals --mutect-low-memory"
// }
// process {
// """
// input[0] = [
// [ id:'test', tumor_id:'tumour' ],
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
// file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
// [],
// [],
// file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
// ]
// input[1] = [ // fasta
// [ id: 'reference' ],
// file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
// ]
// input[2] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
// input[3] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
// """
// }
// }

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

// }

test("human - bam - stub") {

options '-stub'

when {
process {
"""
input[0] = [
[ id:'test', tumor_id:'tumour' ],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
[], // index only neeeded if using intervals or tumor-normal calling
[],
[],
[]
]
input[1] = [ // fasta
[ id: 'reference' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
]
input[2] = [] // pon
input[3] = [] // pon index
"""
}
}

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

}

test("human - bam - pon - stub") {

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

when {
params {
module_args = "--pon $panel_of_normals --mutect-low-memory"
}
process {
"""
input[0] = [
[ id:'test', tumor_id:'tumour' ],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
[],
[],
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
]
input[1] = [ // fasta
[ id: 'reference' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
]
input[2] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
input[3] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
"""
}
}

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

}

}
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