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Merged
merged 2 commits into from
Oct 1, 2025
Merged

update varlociraptor #9162

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69640ec
update varlociraptor
famosab Oct 1, 2025
1bec63a
Merge branch 'master' into vcu
famosab Oct 1, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/varlociraptor/callvariants/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/varlociraptor
- bioconda::varlociraptor=8.7.4
- bioconda::varlociraptor=8.8.0
16 changes: 8 additions & 8 deletions modules/nf-core/varlociraptor/callvariants/main.nf
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Expand Up @@ -3,29 +3,29 @@ process VARLOCIRAPTOR_CALLVARIANTS {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d2/d2431fb9ebb3f21e639fb2e902619752eb6cea81e577b1694ba280704ecc08b0/data':
'community.wave.seqera.io/library/varlociraptor:8.7.4--1d51725b87d202f0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c99922d373e15a47f7a4ad4692e859f99e97a00c7872214903e655f66019c772/data'
: 'community.wave.seqera.io/library/varlociraptor:8.8.0--0d1bd46f0f5e39af'}"

input:
tuple val(meta), path(vcfs)
path (scenario)
val (scenario_aliases)
path scenario
val scenario_aliases

output:
tuple val(meta), path("*.bcf"), emit: bcf
path "versions.yml" , emit: versions
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}_called"

//If we use a scenario file and if there is more than 1 vcf, then collect scenario_aliaes and vcfs to scenario_alias_0=vcf_0 scenario_alias_1=vcf_1, etc
//If we use a scenario file and if there is exactly 1 vcf, then scenario_alias=vcf
def scenario_samples = vcfs instanceof List && vcfs.size() > 1 ? [scenario_aliases,vcfs].transpose().collect{"${it[0]}=${it[1]}"}.join(' ') : "${scenario_aliases}=${vcfs}"
def scenario_samples = vcfs instanceof List && vcfs.size() > 1 ? [scenario_aliases, vcfs].transpose().collect { "${it[0]}=${it[1]}" }.join(' ') : "${scenario_aliases}=${vcfs}"
"""
varlociraptor call variants \\
--output ${prefix}.bcf \\
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20 changes: 10 additions & 10 deletions modules/nf-core/varlociraptor/callvariants/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
]
],
"1": [
"versions.yml:md5,3197a0bb82b8537af6d5e76f23850467"
"versions.yml:md5,4eaf90065308d13ab85f99ab09316186"
],
"bcf": [
[
Expand All @@ -22,55 +22,55 @@
]
],
"versions": [
"versions.yml:md5,3197a0bb82b8537af6d5e76f23850467"
"versions.yml:md5,4eaf90065308d13ab85f99ab09316186"
]
},
{
"VARLOCIRAPTOR_CALLVARIANTS": {
"varlociraptor": "8.7.4"
"varlociraptor": "8.8.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-09-15T12:02:05.695128"
"timestamp": "2025-10-01T10:27:09.972817"
},
"scenario_singlesample": {
"content": [
"test_normal_called.bcf",
[
"versions.yml:md5,3197a0bb82b8537af6d5e76f23850467"
"versions.yml:md5,4eaf90065308d13ab85f99ab09316186"
],
{
"VARLOCIRAPTOR_CALLVARIANTS": {
"varlociraptor": "8.7.4"
"varlociraptor": "8.8.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-09-15T10:32:33.684602"
"timestamp": "2025-10-01T10:26:41.742478"
},
"normal_multisample": {
"content": [
"test_normal_called.bcf",
[
"versions.yml:md5,3197a0bb82b8537af6d5e76f23850467"
"versions.yml:md5,4eaf90065308d13ab85f99ab09316186"
],
{
"VARLOCIRAPTOR_CALLVARIANTS": {
"varlociraptor": "8.7.4"
"varlociraptor": "8.8.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-09-15T10:32:45.823749"
"timestamp": "2025-10-01T10:26:54.57257"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/varlociraptor
- bioconda::varlociraptor=8.7.4
- bioconda::varlociraptor=8.8.0
8 changes: 4 additions & 4 deletions modules/nf-core/varlociraptor/estimatealignmentproperties/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ process VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d2/d2431fb9ebb3f21e639fb2e902619752eb6cea81e577b1694ba280704ecc08b0/data':
'community.wave.seqera.io/library/varlociraptor:8.7.4--1d51725b87d202f0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c99922d373e15a47f7a4ad4692e859f99e97a00c7872214903e655f66019c772/data'
: 'community.wave.seqera.io/library/varlociraptor:8.8.0--0d1bd46f0f5e39af'}"

input:
tuple val(meta), path(bam), path(bai)
Expand All @@ -14,7 +14,7 @@ process VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES {

output:
tuple val(meta), path("*.alignment-properties.json"), emit: alignment_properties_json
path "versions.yml" , emit: versions
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/varlociraptor/estimatealignmentproperties/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
"content": [
"3ac1018cc57d06525ec4336aaad6c7dd",
[
"versions.yml:md5,ee24469102088e02d4eca01536edc2b8"
"versions.yml:md5,d7a4f5c260fb65b832145e17c59238e6"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-09-15T13:36:15.58577"
"timestamp": "2025-10-01T10:28:26.519402"
},
"sarscov2 - [bam,fasta] - stub": {
"content": [
Expand All @@ -25,7 +25,7 @@
]
],
"1": [
"versions.yml:md5,ee24469102088e02d4eca01536edc2b8"
"versions.yml:md5,d7a4f5c260fb65b832145e17c59238e6"
],
"alignment_properties_json": [
[
Expand All @@ -37,19 +37,19 @@
]
],
"versions": [
"versions.yml:md5,ee24469102088e02d4eca01536edc2b8"
"versions.yml:md5,d7a4f5c260fb65b832145e17c59238e6"
]
},
{
"VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES": {
"varlociraptor": "8.7.4"
"varlociraptor": "8.8.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-09-15T12:02:16.049391"
"timestamp": "2025-10-01T10:28:37.78997"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/varlociraptor/preprocess/environment.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/varlociraptor
- bioconda::varlociraptor=8.7.4
- bioconda::varlociraptor=8.8.0
10 changes: 5 additions & 5 deletions modules/nf-core/varlociraptor/preprocess/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ process VARLOCIRAPTOR_PREPROCESS {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d2/d2431fb9ebb3f21e639fb2e902619752eb6cea81e577b1694ba280704ecc08b0/data':
'community.wave.seqera.io/library/varlociraptor:8.7.4--1d51725b87d202f0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c99922d373e15a47f7a4ad4692e859f99e97a00c7872214903e655f66019c772/data'
: 'community.wave.seqera.io/library/varlociraptor:8.8.0--0d1bd46f0f5e39af'}"

input:
tuple val(meta), path(bam), path(bai), path(candidates), path(alignment_json)
Expand All @@ -14,13 +14,13 @@ process VARLOCIRAPTOR_PREPROCESS {

output:
tuple val(meta), path("*.bcf"), emit: bcf
path "versions.yml" , emit: versions
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def alignment_properties_json = alignment_json ? "--alignment-properties ${alignment_json}" : ""
"""
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-core/varlociraptor/preprocess/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
"content": [
"test.bcf",
[
"versions.yml:md5,38d683b9e79eef96c45f3689338f8240"
"versions.yml:md5,fde9d74757426bfa50d49e4877cfda33"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.3"
},
"timestamp": "2025-09-15T11:58:49.48175"
"timestamp": "2025-10-01T10:29:02.03984"
},
"sarscov2 - [bam,vcf,json,fasta] - stub": {
"content": [
Expand All @@ -24,7 +24,7 @@
]
],
"1": [
"versions.yml:md5,38d683b9e79eef96c45f3689338f8240"
"versions.yml:md5,fde9d74757426bfa50d49e4877cfda33"
],
"bcf": [
[
Expand All @@ -35,12 +35,12 @@
]
],
"versions": [
"versions.yml:md5,38d683b9e79eef96c45f3689338f8240"
"versions.yml:md5,fde9d74757426bfa50d49e4877cfda33"
]
},
{
"VARLOCIRAPTOR_PREPROCESS": {
"varlociraptor": "8.7.4"
"varlociraptor": "8.8.0"
}
}
],
Expand Down
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