diff --git a/conf/awsbatch.config b/conf/awsbatch.config index 2e5f83c..a8b61b8 100644 --- a/conf/awsbatch.config +++ b/conf/awsbatch.config @@ -7,10 +7,22 @@ params { awsqueue = false awsregion = 'eu-west-1' awscli = '/home/ec2-user/miniconda/bin/aws' - tracedir = './' +} + +timeline { + overwrite = true +} +report { + overwrite = true +} +trace { + overwrite = true +} +dag { + overwrite = true } process.executor = 'awsbatch' process.queue = params.awsqueue aws.region = params.awsregion -executor.awscli = params.awscli +aws.batch.cliPath = params.awscli diff --git a/conf/jax.config b/conf/jax.config index a5437e9..7cf790e 100644 --- a/conf/jax.config +++ b/conf/jax.config @@ -2,6 +2,7 @@ params { config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.' config_profile_contact = 'Asaf Peer (@peera)' config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx' + singularity_cache_dir = '/fastscratch/singularity_cache_nfcore' } executor.$slurm.queueSize = 250 @@ -12,8 +13,11 @@ process { module = "slurm" beforeScript = 'module load singularity' } -singularity.enabled = true -singularity.autoMounts = true +singularity{ + enabled = true + autoMounts = true + cacheDir = params.singularity_cache_dir +} params { max_memory = 768.GB max_cpus = 70 diff --git a/docs/awsbatch.md b/docs/awsbatch.md index c00acef..daf425b 100644 --- a/docs/awsbatch.md +++ b/docs/awsbatch.md @@ -1,4 +1,6 @@ # nf-core/configs: awsbatch Configuration To be used with `awsbatch`. -Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively. +Custom queue and region can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively. + +Allow `overwrite` of `trace`, `timeline`, `report` and `dag` to allow resuming pipelines.