diff --git a/src/nextflow.config b/src/nextflow.config index 20c5d30739f87e341bdba8b07eab53fb2279ae88..97a988340999a0aaa4dba20700285a874bbe7603 100644 --- a/src/nextflow.config +++ b/src/nextflow.config @@ -85,39 +85,32 @@ profiles { } psmn { charliecloud.enabled = true - cacheDir = "/Xnfs/abc/charliecloud" - runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home" - readOnlyInputs = true + charliecloud.cacheDir = "/Xnfs/abc/charliecloud" + charliecloud.readOnlyInputs = true process{ errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' } maxRetries = 3 + executor = "slurm" + queue = "Lake" withLabel: big_mem_mono_cpus { - executor = "slurm" cpus = 1 memory = "128GB" time = "24h" - clusterOptions = "--partition=Lake" } withLabel: big_mem_multi_cpus { - executor = "slurm" cpus = 32 memory = "192GB" time = "24h" - clusterOptions = "--partition=Lake" } withLabel: small_mem_mono_cpus { - executor = "slurm" cpus = 1 memory = "16GB" time = "24h" - clusterOptions = "--partition=Lake" } withLabel: small_mem_multi_cpus { - executor = "slurm" cpus = 32 memory = "16GB" time = "24h" - clusterOptions = "--partition=Lake" } } }