From faa1c7f5e12561ff440bbbce33ef4d79a05feb6b Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Tue, 7 Apr 2026 13:43:43 +0200 Subject: [PATCH 1/3] CRG --- conf/pipeline/deepmodeloptim/crg.config | 2 +- conf/pipeline/multiplesequencealign/crg.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/deepmodeloptim/crg.config b/conf/pipeline/deepmodeloptim/crg.config index cfa193dea..983e1a03b 100644 --- a/conf/pipeline/deepmodeloptim/crg.config +++ b/conf/pipeline/deepmodeloptim/crg.config @@ -15,7 +15,7 @@ profiles { singularity { enabled = true envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES" - if (params.use_gpu) { singularity.runOptions = '--nv' } + runOptions = params.use_gpu ? '--nv' : '' pullTimeout = "60m" } } diff --git a/conf/pipeline/multiplesequencealign/crg.config b/conf/pipeline/multiplesequencealign/crg.config index 791e56b2f..ca75f617e 100644 --- a/conf/pipeline/multiplesequencealign/crg.config +++ b/conf/pipeline/multiplesequencealign/crg.config @@ -14,7 +14,7 @@ profiles { singularity { enabled = true envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES" - if (params.use_gpu) { singularity.runOptions = '--nv' } + runOptions = params.use_gpu ? '--nv' : '' pullTimeout = "60m" } } From be84c2a427db80360afb0991242e589e878f49c3 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 Apr 2026 13:59:56 +0200 Subject: [PATCH 2/3] Apply suggestions from code review Co-authored-by: Maxime U Garcia --- conf/pipeline/deepmodeloptim/crg.config | 2 +- conf/pipeline/multiplesequencealign/crg.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/deepmodeloptim/crg.config b/conf/pipeline/deepmodeloptim/crg.config index 983e1a03b..4efda6bff 100644 --- a/conf/pipeline/deepmodeloptim/crg.config +++ b/conf/pipeline/deepmodeloptim/crg.config @@ -15,7 +15,7 @@ profiles { singularity { enabled = true envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES" - runOptions = params.use_gpu ? '--nv' : '' + runOptions = params.get('use_gpu', false) ? '--nv' : '' pullTimeout = "60m" } } diff --git a/conf/pipeline/multiplesequencealign/crg.config b/conf/pipeline/multiplesequencealign/crg.config index ca75f617e..255e876bf 100644 --- a/conf/pipeline/multiplesequencealign/crg.config +++ b/conf/pipeline/multiplesequencealign/crg.config @@ -14,7 +14,7 @@ profiles { singularity { enabled = true envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES" - runOptions = params.use_gpu ? '--nv' : '' + runOptions = params.get('use_gpu', false) ? '--nv' : '' pullTimeout = "60m" } } From 02292fdd0043647601b9e6f67386467b8ab95009 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 7 Apr 2026 14:13:57 +0200 Subject: [PATCH 3/3] Apply suggestions from code review Co-authored-by: Maxime U Garcia --- conf/pipeline/deepmodeloptim/crg.config | 2 +- conf/pipeline/multiplesequencealign/crg.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/deepmodeloptim/crg.config b/conf/pipeline/deepmodeloptim/crg.config index 4efda6bff..aec61eb53 100644 --- a/conf/pipeline/deepmodeloptim/crg.config +++ b/conf/pipeline/deepmodeloptim/crg.config @@ -15,7 +15,7 @@ profiles { singularity { enabled = true envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES" - runOptions = params.get('use_gpu', false) ? '--nv' : '' + runOptions = params.contains('use_gpu') && params.use_gpu ? '--nv' : '' pullTimeout = "60m" } } diff --git a/conf/pipeline/multiplesequencealign/crg.config b/conf/pipeline/multiplesequencealign/crg.config index 255e876bf..f0ddf1655 100644 --- a/conf/pipeline/multiplesequencealign/crg.config +++ b/conf/pipeline/multiplesequencealign/crg.config @@ -14,7 +14,7 @@ profiles { singularity { enabled = true envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES" - runOptions = params.get('use_gpu', false) ? '--nv' : '' + runOptions = params.contains('use_gpu') && params.use_gpu ? '--nv' : '' pullTimeout = "60m" } }