Merge pull request #2 from nf-core/master

Merge commits from nf-core/configs master

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

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

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.