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Fix for issue #5021 verifybamid2 module #9563

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Fix for issue #5021 verifybamid2 module #9563

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1f4a60b
updating input suffix check for reference file input, including nf-tests
mmYeung Dec 12, 2025
9f59b2b
Merge branch 'master' into fix/verifybamid/verifybamid2
mmYeung Dec 14, 2025
8547831
Merge branch 'master' into fix/verifybamid/verifybamid2
SPPearce Dec 31, 2025
9ee05e0
Merge branch 'master' into fix/verifybamid/verifybamid2
mmYeung Jan 4, 2026
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13 changes: 7 additions & 6 deletions modules/nf-core/verifybamid/verifybamid2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ process VERIFYBAMID_VERIFYBAMID2 {
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' :
'biocontainers/verifybamid2:2.0.1--h19d48f6_8' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6'
: 'biocontainers/verifybamid2:2.0.1--h19d48f6_8'}"

input:
tuple val(meta), path(bam), path(bai)
Expand Down Expand Up @@ -36,12 +36,13 @@ process VERIFYBAMID_VERIFYBAMID2 {
"--SVDPrefix ${svd_ud.baseName}" : "--UDPath ${svd_ud} --MeanPath ${svd_mu} --BedPath ${svd_bed}"
def refvcf_args = "${refvcf}".endsWith(".vcf") ? "--RefVCF ${refvcf}" : ""

def reference_args = ("$references".endsWith('.fasta')) ?
"--Reference ${references}" : ''
def reference_args = "${references}".matches(/.+((fasta)|(fa)|(fna))(\.gz)*$/)
? "--Reference ${references}"
: ''

"""
verifybamid2 \\
--NumThread $task.cpus \\
--NumThread ${task.cpus} \\
${svd_args} \\
${bam_file} \\
${refvcf_args} \\
Expand Down
59 changes: 59 additions & 0 deletions modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ nextflow_process {
}
}


test("Should run with panel input") {
config "./nextflow.config"

Expand Down Expand Up @@ -177,4 +178,62 @@ nextflow_process {
)
}
}

test("Should run with alternative .fa reference input -stub") {
config "./nextflow.config"

when {
process {
"""
input[0] = [ [ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ]
input[1] = [ [], [], [] ]
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf')
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz')
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.log[0][1]).name,
process.out.bed,
process.out.mu,
process.out.self_sm,
process.out.ancestry,
process.out.versions,
file(process.out.ud[0][1]).name
).match() }
)
}
}

test("Should run with alternative .fa reference input") {
config "./nextflow.config"

options "-stub"

when {
process {
"""
input[0] = [ [ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ]
input[1] = [ [], [], [] ]
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf')
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz')
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
151 changes: 151 additions & 0 deletions modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,42 @@
{
"Should run with alternative .fa reference input -stub": {
"content": [
"test.log",
[
[
{
"id": "test",
"single_end": false
},
"test.genome.vcf.bed:md5,47106c764019ee359b1936410e2efa1e"
]
],
[
[
{
"id": "test",
"single_end": false
},
"test.genome.vcf.mu:md5,0810db02af2a176fa5ddc0f404911b66"
]
],
[

],
[

],
[
"versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
],
"test.genome.vcf.UD"
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-12-12T12:09:25.523364"
},
"Should run with panel input": {
"content": [
"test.log",
Expand Down Expand Up @@ -238,6 +276,119 @@
},
"timestamp": "2025-05-05T16:45:57.687144464"
},
"Should run with alternative .fa reference input": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [

],
"2": [
[
{
"id": "test",
"single_end": false
},
"test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
[
{
"id": "test",
"single_end": false
},
"test.mu:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
[
{
"id": "test",
"single_end": false
},
"test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"5": [
[
{
"id": "test",
"single_end": false
},
"test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"6": [
"versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
],
"ancestry": [
[
{
"id": "test",
"single_end": false
},
"test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"bed": [
[
{
"id": "test",
"single_end": false
},
"test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"log": [
[
{
"id": "test",
"single_end": false
},
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"mu": [
[
{
"id": "test",
"single_end": false
},
"test.mu:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"self_sm": [
[
{
"id": "test",
"single_end": false
},
"test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"ud": [

],
"versions": [
"versions.yml:md5,199f2e02b570926d6a249055c917c6b1"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-12-12T12:28:45.106596"
},
"Should run with SVD input": {
"content": [
{
Expand Down
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