From 500b42fe70594f4726ba7e7627814f8555eb22b7 Mon Sep 17 00:00:00 2001 From: Gary Burnett Date: Wed, 22 Jul 2026 14:15:39 -0700 Subject: [PATCH] feat: bump version to Parabricks 4.7.1 and update snapshots --- modules/nf-core/parabricks/README.md | 2 +- modules/nf-core/parabricks/applybqsr/main.nf | 2 +- .../applybqsr/tests/main.nf.test.snap | 14 +- modules/nf-core/parabricks/dbsnp/main.nf | 2 +- .../parabricks/dbsnp/tests/main.nf.test.snap | 14 +- .../nf-core/parabricks/deepvariant/main.nf | 2 +- .../deepvariant/tests/main.nf.test.snap | 290 +++++++++--------- modules/nf-core/parabricks/fq2bam/main.nf | 2 +- .../parabricks/fq2bam/tests/main.nf.test.snap | 40 +-- modules/nf-core/parabricks/fq2bammeth/main.nf | 2 +- .../fq2bammeth/tests/main.nf.test.snap | 10 +- .../nf-core/parabricks/genotypegvcf/main.nf | 2 +- .../genotypegvcf/tests/main.nf.test.snap | 6 +- .../parabricks/haplotypecaller/main.nf | 2 +- .../haplotypecaller/tests/main.nf.test.snap | 28 +- modules/nf-core/parabricks/indexgvcf/main.nf | 2 +- .../indexgvcf/tests/main.nf.test.snap | 28 +- modules/nf-core/parabricks/minimap2/main.nf | 2 +- .../minimap2/tests/main.nf.test.snap | 86 +++--- .../nf-core/parabricks/mutectcaller/main.nf | 2 +- .../mutectcaller/tests/main.nf.test.snap | 28 +- modules/nf-core/parabricks/rnafq2bam/main.nf | 2 +- .../rnafq2bam/tests/main.nf.test.snap | 12 +- modules/nf-core/parabricks/starfusion/main.nf | 2 +- .../starfusion/tests/main.nf.test.snap | 8 +- 25 files changed, 295 insertions(+), 295 deletions(-) diff --git a/modules/nf-core/parabricks/README.md b/modules/nf-core/parabricks/README.md index 02c41eff156e..e714c8800c45 100644 --- a/modules/nf-core/parabricks/README.md +++ b/modules/nf-core/parabricks/README.md @@ -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 diff --git a/modules/nf-core/parabricks/applybqsr/main.nf b/modules/nf-core/parabricks/applybqsr/main.nf index 40d87d5caae9..11ce0f2bae12 100644 --- a/modules/nf-core/parabricks/applybqsr/main.nf +++ b/modules/nf-core/parabricks/applybqsr/main.nf @@ -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) diff --git a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap index 30bf578d8ad3..621741ae9458 100644 --- a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap @@ -22,7 +22,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -45,7 +45,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -65,7 +65,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -99,7 +99,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -122,7 +122,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -142,7 +142,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -162,7 +162,7 @@ [ "PARABRICKS_APPLYBQSR", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/dbsnp/main.nf b/modules/nf-core/parabricks/dbsnp/main.nf index 0fd395956d6e..f1ba335ef03c 100644 --- a/modules/nf-core/parabricks/dbsnp/main.nf +++ b/modules/nf-core/parabricks/dbsnp/main.nf @@ -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) diff --git a/modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap b/modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap index bf07ef206cf1..fbb2fba6217a 100644 --- a/modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/dbsnp/tests/main.nf.test.snap @@ -7,7 +7,7 @@ [ "PARABRICKS_DBSNP", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -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": [ [ @@ -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" } @@ -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" } } \ No newline at end of file diff --git a/modules/nf-core/parabricks/deepvariant/main.nf b/modules/nf-core/parabricks/deepvariant/main.nf index 60dc9df4a555..86c3b404b0b0 100644 --- a/modules/nf-core/parabricks/deepvariant/main.nf +++ b/modules/nf-core/parabricks/deepvariant/main.nf @@ -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) diff --git a/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap index c62ac2ff45f2..cb693d097a0d 100644 --- a/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap @@ -109,7 +109,7 @@ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -135,17 +135,17 @@ ], "2": [ - "compatible_versions.yml:md5,dbd6540b88f488accb37d270fa4b6bd1" + "compatible_versions.yml:md5,68b2cf8e6a93e78f1abb7487b94c60b8" ], "3": [ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,dbd6540b88f488accb37d270fa4b6bd1" + "compatible_versions.yml:md5,68b2cf8e6a93e78f1abb7487b94c60b8" ], "gvcf": [ @@ -162,13 +162,13 @@ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_DEEPVARIANT": { - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": { "DeepVariant:": "1.9.0" } @@ -179,110 +179,110 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:57:11.632600274" + "timestamp": "2026-07-22T13:55:20.9987153" }, "human - bam - intervals": { "content": [ [ "chr21\t6118303\t.\tC\tG\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:15:12:10,2:0.166667:0,15,22", "chr21\t6118347\t.\tG\tT\t0.3\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:12:11:9,2:0.181818:0,12,19", - 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"4.7.0-1" + "4.7.1-1" ] ] } @@ -299,110 +299,110 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:56:31.704139318" + "timestamp": "2026-07-22T13:54:43.339144689" }, "human - bam": { "content": [ [ "chr21\t6118303\t.\tC\tG\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:15:12:10,2:0.166667:0,15,22", "chr21\t6118347\t.\tG\tT\t0.3\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:12:11:9,2:0.181818:0,12,19", - "chr21\t6118556\t.\tT\tG\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:16:8:6,2:0.25:0,17,21", - "chr21\t6118720\t.\tT\tG\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:17:7:5,2:0.285714:0,17,22", + "chr21\t6118556\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:23:8:6,2:0.25:small_model:0,25,25", + "chr21\t6118720\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:22:7:5,2:0.285714:small_model:0,25,23", "chr21\t6120003\t.\tT\tA\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:17:14:12,2:0.142857:0,17,23", "chr21\t6120024\t.\tT\tA\t0.3\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:12:13:11,2:0.153846:0,12,20", "chr21\t6120030\t.\tC\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:20:13:11,2:0.153846:0,21,24", "chr21\t6120072\t.\tA\tC\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:19:8:6,2:0.25:0,21,22", - 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"chr21\t10539156\t.\tG\tC\t0.3\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:11:12:10,2:0.166667:0,11,24", - "chr21\t10539199\t.\tG\tC\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:20:11:9,2:0.181818:0,21,24", - "chr21\t10539215\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:21:9:7,2:0.222222:0,23,24", - "chr21\t10541372\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:22:16:14,2:0.125:0,24,24", - "chr21\t10541384\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:22:16:14,2:0.125:0,24,24", - "chr21\t10541585\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:21:25:22,3:0.12:0,23,24", - "chr21\t10541615\t.\tT\tG\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:15:20:17,3:0.15:0,15,23", - "chr21\t10541650\t.\tT\tG\t0.1\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:18:11:9,2:0.181818:0,18,24", - "chr21\t10541704\t.\tA\tT\t0.3\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:12:6:4,2:0.333333:0,11,22", - "chr21\t10542594\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:20:15:13,2:0.133333:0,22,24", - "chr21\t10542621\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:22:16:14,2:0.125:0,24,24", - "chr21\t10542681\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t0/0:22:15:13,2:0.133333:0,24,24", + "chr21\t7820041\t.\tC\tA\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:32:15:12,2:0.133333:small_model:0,33,36", + "chr21\t10538700\t.\tT\tA\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:47:17:14,3:0.176471:small_model:0,46,99", + "chr21\t10538961\t.\tG\tC\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:51:16:14,2:0.125:small_model:0,51,71", + "chr21\t10539145\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:40:12:9,3:0.25:small_model:0,40,54", + "chr21\t10539156\t.\tG\tC\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:39:12:10,2:0.166667:small_model:0,39,52", + "chr21\t10539199\t.\tG\tC\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:27:11:9,2:0.181818:small_model:0,27,40", + "chr21\t10539215\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:24:9:7,2:0.222222:small_model:0,24,38", + "chr21\t10541372\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:53:16:14,2:0.125:small_model:0,53,65", + "chr21\t10541384\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:55:16:14,2:0.125:small_model:0,55,70", + "chr21\t10541585\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:60:25:22,3:0.12:small_model:0,60,77", + "chr21\t10541615\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:51:20:17,3:0.15:small_model:0,51,64", + "chr21\t10541650\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:36:11:9,2:0.181818:small_model:0,36,55", + "chr21\t10541704\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:23:6:4,2:0.333333:small_model:0,23,36", + "chr21\t10542594\t.\tT\tG\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:38:15:13,2:0.133333:small_model:0,37,54", + "chr21\t10542621\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:43:16:14,2:0.125:small_model:0,42,61", + "chr21\t10542681\t.\tA\tT\t0\tRefCall\t.\tGT:GQ:DP:AD:VAF:MID:PL\t0/0:57:15:13,2:0.133333:small_model:0,56,75", "chr21\t10542821\t.\tG\tC\t0.7\tRefCall\t.\tGT:GQ:DP:AD:VAF:PL\t./.:8:8:6,2:0.25:0,7,22" ], { @@ -410,7 +410,7 @@ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -419,7 +419,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:56:15.037289899" + "timestamp": "2026-07-22T13:54:27.267963808" }, "human - bam - intervals - gvcf - stub": { "content": [ @@ -441,17 +441,17 @@ ] ], "2": [ - "compatible_versions.yml:md5,dbd6540b88f488accb37d270fa4b6bd1" + "compatible_versions.yml:md5,68b2cf8e6a93e78f1abb7487b94c60b8" ], "3": [ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,dbd6540b88f488accb37d270fa4b6bd1" + "compatible_versions.yml:md5,68b2cf8e6a93e78f1abb7487b94c60b8" ], "gvcf": [ [ @@ -473,7 +473,7 @@ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -482,7 +482,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:57:21.609551822" + "timestamp": "2026-07-22T13:55:28.742123322" }, "human - bam - gvcf": { "content": [ @@ -594,7 +594,7 @@ [ "PARABRICKS_DEEPVARIANT", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/fq2bam/main.nf b/modules/nf-core/parabricks/fq2bam/main.nf index 3586174521c4..11ed6f53611f 100644 --- a/modules/nf-core/parabricks/fq2bam/main.nf +++ b/modules/nf-core/parabricks/fq2bam/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_FQ2BAM { // needed by the module to run on a cluster because we need to copy the fasta reference, see https://github.com/nf-core/modules/issues/9230 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(reads) diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap index 4eff07694cb9..bbdad1c2f5e5 100644 --- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap @@ -36,13 +36,13 @@ ], "7": [ - "compatible_versions.yml:md5,daf8cc0f6110c611f9f71e2a5c50e96c" + "compatible_versions.yml:md5,c48631d6ae7f0acd46e4c08881c0cde4" ], "8": [ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -67,7 +67,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,daf8cc0f6110c611f9f71e2a5c50e96c" + "compatible_versions.yml:md5,c48631d6ae7f0acd46e4c08881c0cde4" ], "crai": [ @@ -85,13 +85,13 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_FQ2BAM": null, - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": "BWA mem: 0.7.15, Picard: 2.18.25" } ], @@ -99,7 +99,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:57:54.537127867" + "timestamp": "2026-07-22T13:56:25.919782719" }, "sarscov2 - fastq - pe - stub": { "content": [ @@ -138,13 +138,13 @@ ], "7": [ - "compatible_versions.yml:md5,daf8cc0f6110c611f9f71e2a5c50e96c" + "compatible_versions.yml:md5,c48631d6ae7f0acd46e4c08881c0cde4" ], "8": [ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -169,7 +169,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,daf8cc0f6110c611f9f71e2a5c50e96c" + "compatible_versions.yml:md5,c48631d6ae7f0acd46e4c08881c0cde4" ], "crai": [ @@ -187,13 +187,13 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_FQ2BAM": null, - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": "BWA mem: 0.7.15, Picard: 2.18.25" } ], @@ -201,7 +201,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:58:20.084300726" + "timestamp": "2026-07-22T13:57:20.850459502" }, "sarscov2 - fastq - pe": { "content": [ @@ -212,7 +212,7 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -232,7 +232,7 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -280,13 +280,13 @@ ], "7": [ - "compatible_versions.yml:md5,daf8cc0f6110c611f9f71e2a5c50e96c" + "compatible_versions.yml:md5,c48631d6ae7f0acd46e4c08881c0cde4" ], "8": [ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -299,7 +299,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,daf8cc0f6110c611f9f71e2a5c50e96c" + "compatible_versions.yml:md5,c48631d6ae7f0acd46e4c08881c0cde4" ], "crai": [ [ @@ -329,7 +329,7 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -338,7 +338,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T07:58:45.441327996" + "timestamp": "2026-07-22T13:58:14.974718817" }, "SRR389222 - fastq - se": { "content": [ @@ -349,7 +349,7 @@ [ "PARABRICKS_FQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf index e74b879d7186..2d7b37bf0f36 100644 --- a/modules/nf-core/parabricks/fq2bammeth/main.nf +++ b/modules/nf-core/parabricks/fq2bammeth/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_FQ2BAMMETH { // 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(reads) diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap index 67aa480ab5c6..3a47292b8f4e 100644 --- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap @@ -33,7 +33,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -67,7 +67,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -112,7 +112,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -146,7 +146,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -174,7 +174,7 @@ [ "PARABRICKS_FQ2BAMMETH", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/genotypegvcf/main.nf b/modules/nf-core/parabricks/genotypegvcf/main.nf index 01a1145c1981..d40058b7922e 100644 --- a/modules/nf-core/parabricks/genotypegvcf/main.nf +++ b/modules/nf-core/parabricks/genotypegvcf/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_GENOTYPEGVCF { // 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) diff --git a/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap b/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap index f7cffb37d54e..fbacc5e413b2 100644 --- a/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/genotypegvcf/tests/main.nf.test.snap @@ -7,7 +7,7 @@ [ "PARABRICKS_GENOTYPEGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -34,7 +34,7 @@ [ "PARABRICKS_GENOTYPEGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "vcf": [ @@ -50,7 +50,7 @@ [ "PARABRICKS_GENOTYPEGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/haplotypecaller/main.nf b/modules/nf-core/parabricks/haplotypecaller/main.nf index 17bec68694f3..9efff97226ed 100644 --- a/modules/nf-core/parabricks/haplotypecaller/main.nf +++ b/modules/nf-core/parabricks/haplotypecaller/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_HAPLOTYPECALLER { // 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) diff --git a/modules/nf-core/parabricks/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/parabricks/haplotypecaller/tests/main.nf.test.snap index 28f5d3a41259..d9d3434abdab 100644 --- a/modules/nf-core/parabricks/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/haplotypecaller/tests/main.nf.test.snap @@ -24,17 +24,17 @@ ], "2": [ - "compatible_versions.yml:md5,bccbd04b9cc3fe86310c65de87f68bce" + "compatible_versions.yml:md5,f33bcfc78fef1f8b1314c038eca05930" ], "3": [ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,bccbd04b9cc3fe86310c65de87f68bce" + "compatible_versions.yml:md5,f33bcfc78fef1f8b1314c038eca05930" ], "gvcf": [ @@ -51,13 +51,13 @@ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_HAPLOTYPECALLER": { - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": { "GATK:": "4.3.0.0" } @@ -68,7 +68,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:01:45.579712219" + "timestamp": "2026-07-22T14:00:59.770132188" }, "human - bam - intervals": { "content": [ @@ -78,7 +78,7 @@ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -97,7 +97,7 @@ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -123,17 +123,17 @@ ] ], "2": [ - "compatible_versions.yml:md5,bccbd04b9cc3fe86310c65de87f68bce" + "compatible_versions.yml:md5,f33bcfc78fef1f8b1314c038eca05930" ], "3": [ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,bccbd04b9cc3fe86310c65de87f68bce" + "compatible_versions.yml:md5,f33bcfc78fef1f8b1314c038eca05930" ], "gvcf": [ [ @@ -150,7 +150,7 @@ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -159,7 +159,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:01:54.686762276" + "timestamp": "2026-07-22T14:01:07.652784055" }, "human - bam - gvcf": { "content": [ @@ -169,7 +169,7 @@ [ "PARABRICKS_HAPLOTYPECALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/indexgvcf/main.nf b/modules/nf-core/parabricks/indexgvcf/main.nf index 2bb8bc3e04b4..81aab33947a3 100644 --- a/modules/nf-core/parabricks/indexgvcf/main.nf +++ b/modules/nf-core/parabricks/indexgvcf/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_INDEXGVCF { // 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(gvcf) diff --git a/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap b/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap index 77b426e49518..b2e6819f421c 100644 --- a/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap @@ -17,7 +17,7 @@ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ @@ -35,7 +35,7 @@ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -54,7 +54,7 @@ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -77,17 +77,17 @@ ] ], "1": [ - "compatible_versions.yml:md5,c238cde6963f7e9178a58f9603d7a6ba" + "compatible_versions.yml:md5,ac481933e4706f81716845306ca16eb8" ], "2": [ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,c238cde6963f7e9178a58f9603d7a6ba" + "compatible_versions.yml:md5,ac481933e4706f81716845306ca16eb8" ], "gvcf_index": [ [ @@ -101,13 +101,13 @@ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_INDEXGVCF": { - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": { "GATK:": "4.3.0.0" } @@ -118,7 +118,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:02:25.137037794" + "timestamp": "2026-07-22T14:01:29.013709643" }, "human - gvcf.gz - stub": { "content": [ @@ -132,17 +132,17 @@ ] ], "1": [ - "compatible_versions.yml:md5,c238cde6963f7e9178a58f9603d7a6ba" + "compatible_versions.yml:md5,ac481933e4706f81716845306ca16eb8" ], "2": [ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,c238cde6963f7e9178a58f9603d7a6ba" + "compatible_versions.yml:md5,ac481933e4706f81716845306ca16eb8" ], "gvcf_index": [ [ @@ -156,7 +156,7 @@ [ "PARABRICKS_INDEXGVCF", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -165,6 +165,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:02:33.08091659" + "timestamp": "2026-07-22T14:01:35.805472948" } } \ No newline at end of file diff --git a/modules/nf-core/parabricks/minimap2/main.nf b/modules/nf-core/parabricks/minimap2/main.nf index 8c11b3f28a2c..2b9ca1e0c6fa 100644 --- a/modules/nf-core/parabricks/minimap2/main.nf +++ b/modules/nf-core/parabricks/minimap2/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_MINIMAP2 { // 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(reads) diff --git a/modules/nf-core/parabricks/minimap2/tests/main.nf.test.snap b/modules/nf-core/parabricks/minimap2/tests/main.nf.test.snap index 22953516e503..9bedcc0145ee 100644 --- a/modules/nf-core/parabricks/minimap2/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/minimap2/tests/main.nf.test.snap @@ -8,7 +8,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -28,7 +28,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -76,13 +76,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -95,7 +95,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ [ @@ -125,7 +125,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -134,7 +134,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:06:09.119305778" + "timestamp": "2026-07-22T14:04:51.3729922" }, "homo_sapiens - bam - cram": { "content": [ @@ -145,7 +145,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -199,13 +199,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -236,7 +236,7 @@ ] ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ @@ -254,7 +254,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -263,7 +263,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:05:00.08925079" + "timestamp": "2026-07-22T14:03:47.379018246" }, "homo_sapiens - bam - bam": { "content": [ @@ -274,7 +274,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -328,13 +328,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -365,7 +365,7 @@ ] ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ @@ -383,7 +383,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -392,7 +392,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:04:24.280784153" + "timestamp": "2026-07-22T14:03:14.717094186" }, "homo_sapiens - fastq - bam - interval_file": { "content": [ @@ -414,7 +414,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -434,7 +434,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -482,13 +482,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -513,7 +513,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ @@ -531,7 +531,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -540,7 +540,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:05:34.932153656" + "timestamp": "2026-07-22T14:04:20.415416049" }, "homo_sapiens - fastq - bam - stub": { "content": [ @@ -579,13 +579,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -610,7 +610,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ @@ -628,15 +628,15 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_MINIMAP2": { - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": { - "minimap2": 2.3 + "minimap2": 2.31 } } } @@ -645,7 +645,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:03:14.72008813" + "timestamp": "2026-07-22T14:02:08.253405214" }, "homo_sapiens - bam - cram - stub": { "content": [ @@ -684,13 +684,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -703,7 +703,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ [ @@ -733,7 +733,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -742,7 +742,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:06:42.685049957" + "timestamp": "2026-07-22T14:05:22.701764204" }, "homo_sapiens - fastq - bam - interval_file - stub": { "content": [ @@ -781,13 +781,13 @@ ], "7": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "8": [ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "bai": [ @@ -812,7 +812,7 @@ ], "compatible_versions": [ - "compatible_versions.yml:md5,493cd4518173daa74759a0e8ec95c05b" + "compatible_versions.yml:md5,3848622dd0e65ae30c1f11beaab3d0f1" ], "crai": [ @@ -830,7 +830,7 @@ [ "PARABRICKS_MINIMAP2", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -839,6 +839,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-17T08:03:48.704360504" + "timestamp": "2026-07-22T14:02:40.732861506" } } \ No newline at end of file diff --git a/modules/nf-core/parabricks/mutectcaller/main.nf b/modules/nf-core/parabricks/mutectcaller/main.nf index a476ca2fae58..025c097c3506 100644 --- a/modules/nf-core/parabricks/mutectcaller/main.nf +++ b/modules/nf-core/parabricks/mutectcaller/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_MUTECTCALLER { // 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), val(tumor_name), val(normal_name), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals) diff --git a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap index 88080f555e1a..c8569c1a7be8 100644 --- a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap @@ -22,17 +22,17 @@ ] ], "2": [ - "compatible_versions.yml:md5,2d6eedcfb8cfa31f923ac0fa830d4479" + "compatible_versions.yml:md5,c0e51da32ba7664cc88938bf54d4f806" ], "3": [ [ "PARABRICKS_MUTECTCALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,2d6eedcfb8cfa31f923ac0fa830d4479" + "compatible_versions.yml:md5,c0e51da32ba7664cc88938bf54d4f806" ], "stats": [ [ @@ -57,16 +57,16 @@ [ "PARABRICKS_MUTECTCALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.1" + "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T08:05:46.467440276" + "timestamp": "2026-07-22T14:05:59.071527475" }, "human - bam - stub": { "content": [ @@ -88,17 +88,17 @@ ] ], "2": [ - "compatible_versions.yml:md5,2d6eedcfb8cfa31f923ac0fa830d4479" + "compatible_versions.yml:md5,c0e51da32ba7664cc88938bf54d4f806" ], "3": [ [ "PARABRICKS_MUTECTCALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "compatible_versions": [ - "compatible_versions.yml:md5,2d6eedcfb8cfa31f923ac0fa830d4479" + "compatible_versions.yml:md5,c0e51da32ba7664cc88938bf54d4f806" ], "stats": [ [ @@ -120,13 +120,13 @@ [ "PARABRICKS_MUTECTCALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, { "PARABRICKS_MUTECTCALLER": { - "pbrun_version": "4.7.0-1", + "pbrun_version": "4.7.1-1", "compatible_with": { "GATK:": "4.3.0.0" } @@ -135,9 +135,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.1" + "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T08:05:36.745386073" + "timestamp": "2026-07-22T14:05:50.72227014" }, "human - bam": { "content": [ @@ -155,7 +155,7 @@ [ "PARABRICKS_MUTECTCALLER", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/rnafq2bam/main.nf b/modules/nf-core/parabricks/rnafq2bam/main.nf index 16f1e68654ac..9d78a3a308a4 100644 --- a/modules/nf-core/parabricks/rnafq2bam/main.nf +++ b/modules/nf-core/parabricks/rnafq2bam/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_RNAFQ2BAM { // 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(reads) diff --git a/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test.snap b/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test.snap index 5bd8a125391b..2978600e3f3e 100644 --- a/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test.snap @@ -97,7 +97,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "2": [ @@ -342,7 +342,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "wig": [ @@ -460,7 +460,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "2": [ @@ -705,7 +705,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "wig": [ @@ -733,7 +733,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }, @@ -755,7 +755,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } diff --git a/modules/nf-core/parabricks/starfusion/main.nf b/modules/nf-core/parabricks/starfusion/main.nf index 8eecd31c3e18..5456620f3ffd 100644 --- a/modules/nf-core/parabricks/starfusion/main.nf +++ b/modules/nf-core/parabricks/starfusion/main.nf @@ -5,7 +5,7 @@ process PARABRICKS_STARFUSION { // 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(chimeric_junction) diff --git a/modules/nf-core/parabricks/starfusion/tests/main.nf.test.snap b/modules/nf-core/parabricks/starfusion/tests/main.nf.test.snap index 79285bf93da6..bb78bd8531e8 100644 --- a/modules/nf-core/parabricks/starfusion/tests/main.nf.test.snap +++ b/modules/nf-core/parabricks/starfusion/tests/main.nf.test.snap @@ -24,7 +24,7 @@ [ "PARABRICKS_STARFUSION", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "abridged": [ @@ -49,7 +49,7 @@ [ "PARABRICKS_STARFUSION", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] } @@ -85,7 +85,7 @@ [ "PARABRICKS_STARFUSION", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ], "abridged": [ @@ -110,7 +110,7 @@ [ "PARABRICKS_STARFUSION", "parabricks", - "4.7.0-1" + "4.7.1-1" ] ] }