From fbe78b60ca2557d3c63bf8134166d3a15e4802c2 Mon Sep 17 00:00:00 2001 From: JohannesKersting Date: Fri, 3 Jul 2026 15:00:33 +0200 Subject: [PATCH 1/2] updated gpu profile to support process labels --- conf/daisybio.config | 12 ++++++------ docs/daisybio.md | 16 +++++++++++++++- 2 files changed, 21 insertions(+), 7 deletions(-) diff --git a/conf/daisybio.config b/conf/daisybio.config index 9f6098186..cf7ec3c23 100644 --- a/conf/daisybio.config +++ b/conf/daisybio.config @@ -84,11 +84,11 @@ profiles { docker.runOptions = '-u $(id -u):$(id -g) --gpus all' apptainer.runOptions = '--nv' singularity.runOptions = '--nv' - process.queue = 'shared-gpu' - process.clusterOptions = '--qos=limitgpus --gpus=a40:1 --exclude compms-gpu-1.exbio.wzw.tum.de' - executor.queueSize = 5 + process{ + withLabel:process_gpu { + queue = 'shared-gpu' + clusterOptions = '--qos=limitgpus --gpus=a40:1 --exclude compms-gpu-1.exbio.wzw.tum.de' + } + } } } - - - diff --git a/docs/daisybio.md b/docs/daisybio.md index 5c2cefb43..2a5267c7f 100644 --- a/docs/daisybio.md +++ b/docs/daisybio.md @@ -7,6 +7,20 @@ This will automatically download and apply ['daisybio.config'](../conf/daisybio. The config file will set slurm as a scheduler for the compute cluster, define max resources, and specify cache locations for singularity, apptainer, and iGenomes. Pipeline-specific parameters still need to be configured manually. +## Keep work directories + Work directories will be kept at `/nfs/scratch/nf-core_work/` in a directory named after the full path of the launch directory ("." separated). Thy are automatically removed after a successful pipeline run. To keep the intermediate file, e.g. for using the `-resume` function, add `keep_work` as a profile: `-profile daisybio,,keep_work`. -If you need GPU access, add `gpu` to the profile list to submit to the gpu queue: `-profile daisybio,,gpu`. +## GPU support + +If you need GPU access, add `gpu` to the profile list: `-profile daisybio,,gpu`. +This will submit all processes labeled with `process_gpu` to our GPU queue. +If you are using an nf-core pipeline, processes with GPU support should be already labeled correctly. +If you are using a custom pipeline, you need to add the label to the process definition: + +``` +process YOURGPUPROCESS { + label 'process_gpu' + # ... +} +``` From f7f9d21ff9e4a70d4617a53586099fac6c337fb6 Mon Sep 17 00:00:00 2001 From: JohannesKersting <66471005+JohannesKersting@users.noreply.github.com> Date: Fri, 3 Jul 2026 15:06:34 +0200 Subject: [PATCH 2/2] Typo fix Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- docs/daisybio.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/daisybio.md b/docs/daisybio.md index 2a5267c7f..422474477 100644 --- a/docs/daisybio.md +++ b/docs/daisybio.md @@ -9,7 +9,7 @@ Pipeline-specific parameters still need to be configured manually. ## Keep work directories -Work directories will be kept at `/nfs/scratch/nf-core_work/` in a directory named after the full path of the launch directory ("." separated). Thy are automatically removed after a successful pipeline run. To keep the intermediate file, e.g. for using the `-resume` function, add `keep_work` as a profile: `-profile daisybio,,keep_work`. +Work directories will be kept at `/nfs/scratch/nf-core_work/` in a directory named after the full path of the launch directory ("." separated). They are automatically removed after a successful pipeline run. To keep the intermediate files, e.g. for using the `-resume` function, add `keep_work` as a profile: `-profile daisybio,,keep_work`. ## GPU support