From 5bd29fa44f562daa2e45a6c1205dae0f3f9ad14d Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Fri, 21 Feb 2025 08:46:15 +0000 Subject: [PATCH 1/2] fix singularity config --- nextflow.config | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index cb5f796..eac2c86 100644 --- a/nextflow.config +++ b/nextflow.config @@ -123,22 +123,21 @@ profiles { } docker { docker.enabled = true - docker.runOptions = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)' + docker.runOptions = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)' conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true singularity.autoMounts = true - singularity.runOptions = params.use_gpu ? '--nv' : singularity.runOptions + singularity.runOptions = params.use_gpu ? '--nv' : "" conda.enabled = false docker.enabled = false podman.enabled = false @@ -177,7 +176,7 @@ profiles { apptainer { apptainer.enabled = true apptainer.autoMounts = true - apptainer.runOptions = params.use_gpu ? '--nv' : apptainer.runOptions + apptainer.runOptions = params.use_gpu ? '--nv' : "" conda.enabled = false docker.enabled = false singularity.enabled = false From 439a33c24e16ec97943abc4932940e19a576a5f8 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Fri, 21 Feb 2025 08:51:26 +0000 Subject: [PATCH 2/2] fix lint --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index eac2c86..5a62454 100644 --- a/nextflow.config +++ b/nextflow.config @@ -235,7 +235,6 @@ charliecloud.registry = 'quay.io' // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. - env { PYTHONNOUSERSITE = 1 R_PROFILE_USER = "/.Rprofile"