diff --git a/modules.json b/modules.json index da03048fd..d06d9ab93 100644 --- a/modules.json +++ b/modules.json @@ -141,7 +141,7 @@ }, "parabricks/rnafq2bam": { "branch": "master", - "git_sha": "0c44f69eefe8a8c373c7cdd9528b3e1d60cb895f", + "git_sha": "3e0ec6464725c64d81abe928e15a6750d5fdd272", "installed_by": ["modules"] }, "picard/markduplicates": { diff --git a/modules/nf-core/parabricks/rnafq2bam/main.nf b/modules/nf-core/parabricks/rnafq2bam/main.nf index ddaf70c77..9d78a3a30 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:4.6.0-1" + 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 b/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test index bf79d3150..5423013a0 100644 --- a/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test +++ b/modules/nf-core/parabricks/rnafq2bam/tests/main.nf.test @@ -30,16 +30,13 @@ nextflow_process { } } - test("homo_sapiens") { + config "./nextflow.config" - config "./nextflow.config" + test("homo_sapiens") { when { params { - module_args = '--low-memory --read-files-command zcat --x3' - // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 - // Parabricks’s rnafq2bam requires 24GB of memory. - // Using --low-memory for testing + module_args = '--num-streams-per-gpu 1 --read-files-command zcat --x3' } process { """ @@ -72,7 +69,6 @@ nextflow_process { test("homo_sapiens - stub") { - config "./nextflow.config" options "-stub" when { @@ -106,14 +102,9 @@ nextflow_process { test("homo_sapiens_chimeric") { - config "./nextflow.config" - when { params { - module_args = '--low-memory --read-files-command zcat --out-chim-type Junctions --min-chim-segment 15 --x3' - // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 - // Parabricks’s rnafq2bam requires 24GB of memory. - // Using --low-memory for testing + module_args = '--num-streams-per-gpu 1 --read-files-command zcat --out-chim-type Junctions --min-chim-segment 15 --x3' } process { """ @@ -147,7 +138,6 @@ nextflow_process { test("homo_sapiens_chimeric - stub") { - config "./nextflow.config" options "-stub" when { 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 a0fadd02b..2978600e3 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", - "4.6.0-1" + "4.7.1-1" ] ], "2": [ @@ -342,7 +342,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.6.0-1" + "4.7.1-1" ] ], "wig": [ @@ -358,9 +358,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-09T09:28:46.515275982" + "timestamp": "2026-04-17T08:08:44.920007509" }, "homo_sapiens_chimeric - stub": { "content": [ @@ -460,7 +460,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.6.0-1" + "4.7.1-1" ] ], "2": [ @@ -705,7 +705,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.6.0-1" + "4.7.1-1" ] ], "wig": [ @@ -721,9 +721,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-09T09:29:54.340122816" + "timestamp": "2026-04-17T08:09:51.697962968" }, "homo_sapiens": { "content": [ @@ -733,7 +733,7 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.6.0-1" + "4.7.1-1" ] ] }, @@ -741,9 +741,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-09T09:27:02.147122093" + "timestamp": "2026-04-17T08:08:34.03461553" }, "homo_sapiens_chimeric": { "content": [ @@ -755,15 +755,15 @@ [ "PARABRICKS_RNAFQ2BAM", "parabricks", - "4.6.0-1" + "4.7.1-1" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-09T09:29:44.105218347" + "timestamp": "2026-04-17T08:09:41.244103512" } } \ No newline at end of file diff --git a/modules/nf-core/parabricks/rnafq2bam/tests/nextflow.config b/modules/nf-core/parabricks/rnafq2bam/tests/nextflow.config index 7e550187c..d85565b63 100644 --- a/modules/nf-core/parabricks/rnafq2bam/tests/nextflow.config +++ b/modules/nf-core/parabricks/rnafq2bam/tests/nextflow.config @@ -1,8 +1,11 @@ process { - // Parabricks rnafq2bam requires more memory withName: 'PARABRICKS_RNAFQ2BAM' { - ext.args = params.module_args - accelerator.request = 1 + ext.args = { params.module_args } + accelerator = [request: 1] + // The nf-test config caps system memory usage to 4.GB + // This module requires at least 30 GB to run without error + // Note: The Github runners run highmem GPU tests on a machine with 31 GB available memory + // See .github/workflows/nf-test-gpu.yml for exact machine specs memory = 30.GB } diff --git a/tests/parabricks_default.nf.test.snap b/tests/parabricks_default.nf.test.snap index 9efe10b87..aa211ab68 100644 --- a/tests/parabricks_default.nf.test.snap +++ b/tests/parabricks_default.nf.test.snap @@ -50,7 +50,7 @@ "gunzip": 1.13 }, "PARABRICKS_RNA_FQ2BAM": { - "parabricks": "4.6.0-1" + "parabricks": "4.7.1-1" }, "PARABRICKS_STARGENOMEGENERATE": { "gawk": "5.1.0", @@ -633,9 +633,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "26.04.6" }, - "timestamp": "2026-02-09T11:01:14.364447839" + "timestamp": "2026-07-31T12:53:06.381504124" }, "Params: parabricks star_salmon (with markdups) - stub": { "content": [ @@ -880,7 +880,7 @@ "gunzip": 1.13 }, "PARABRICKS_RNA_FQ2BAM": { - "parabricks": "4.6.0-1" + "parabricks": "4.7.1-1" }, "PARABRICKS_STARGENOMEGENERATE": { "gawk": "5.1.0", @@ -1453,8 +1453,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "26.04.6" }, - "timestamp": "2026-02-09T11:13:00.399098759" + "timestamp": "2026-07-31T12:58:57.904720898" } -} +} \ No newline at end of file