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Update Parabricks modules to version 4.7.1 #12404

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Merged
gburnett-nvidia merged 1 commit into from
Jul 23, 2026
Merged

Update Parabricks modules to version 4.7.1 #12404

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2 changes: 1 addition & 1 deletion modules/nf-core/parabricks/README.md
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Expand Up @@ -4,7 +4,7 @@ These nf-core modules implement functionality of the NVIDIA Parabricks software

## General considerations

Parabricks is available only through a docker container: `nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1`. The main entrypoint to the Parabricks is the command line program `pbrun`, which calls several sub-programs within the container. The Parabricks authors combined several common patterns into a single tool, such as `fq2bam` performing alignment, sorting, mark duplicates, and base quality score recalibration, all within a single command. Generally, the tools can be used for only a subset of the entire functionality as well.
Parabricks is available only through a docker container: `nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1`. The main entrypoint to the Parabricks is the command line program `pbrun`, which calls several sub-programs within the container. The Parabricks authors combined several common patterns into a single tool, such as `fq2bam` performing alignment, sorting, mark duplicates, and base quality score recalibration, all within a single command. Generally, the tools can be used for only a subset of the entire functionality as well.

## Hardware Requirements

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2 changes: 1 addition & 1 deletion modules/nf-core/parabricks/applybqsr/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PARABRICKS_APPLYBQSR {
// needed by the module to work properly can be removed when fixed upstream - see: https://github.com/nf-core/modules/issues/7226
stageInMode 'copy'

container "nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1"
container "nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1"

input:
tuple val(meta), path(bam)
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14 changes: 7 additions & 7 deletions modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
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Expand Up @@ -22,7 +22,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
],
"bai": [
Expand All @@ -45,7 +45,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
}
Expand All @@ -65,7 +65,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
}
Expand Down Expand Up @@ -99,7 +99,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
],
"bai": [
Expand All @@ -122,7 +122,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
}
Expand All @@ -142,7 +142,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
}
Expand All @@ -162,7 +162,7 @@
[
"PARABRICKS_APPLYBQSR",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
}
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2 changes: 1 addition & 1 deletion modules/nf-core/parabricks/dbsnp/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PARABRICKS_DBSNP {
// needed by the module to work properly can be removed when fixed upstream - see: https://github.com/nf-core/modules/issues/7226
stageInMode 'copy'

container "nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1"
container "nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1"

input:
tuple val(meta), path(vcf_file), path(dbsnp_file), path(tabix_file)
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14 changes: 7 additions & 7 deletions modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
[
"PARABRICKS_DBSNP",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
}
Expand All @@ -31,17 +31,17 @@
]
],
"1": [
"compatible_versions.yml:md5,a1244a714c4fcc3ce041e8672bbf2c27"
"compatible_versions.yml:md5,ebf34ae33fe5f95a0797339c7b7af4e1"
],
"2": [
[
"PARABRICKS_DBSNP",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
],
"compatible_versions": [
"compatible_versions.yml:md5,a1244a714c4fcc3ce041e8672bbf2c27"
"compatible_versions.yml:md5,ebf34ae33fe5f95a0797339c7b7af4e1"
],
"vcf": [
[
Expand All @@ -56,13 +56,13 @@
[
"PARABRICKS_DBSNP",
"parabricks",
"4.7.0-1"
"4.7.1-1"
]
]
},
{
"PARABRICKS_DBSNP": {
"pbrun_version": "4.7.0-1",
"pbrun_version": "4.7.1-1",
"compatible_with": {
"GATK:": "4.3.0.0"
}
Expand All @@ -73,6 +73,6 @@
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2026-04-17T07:55:49.545889511"
"timestamp": "2026-07-22T13:54:04.606322563"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/parabricks/deepvariant/main.nf
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Expand Up @@ -5,7 +5,7 @@ process PARABRICKS_DEEPVARIANT {
// needed by the module to work properly can be removed when fixed upstream - see: https://github.com/nf-core/modules/issues/7226
stageInMode 'copy'

container "nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1"
container "nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1"

input:
tuple val(meta), path(input), path(input_index), path(intervals)
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