From 885f0ce5f69abafac3237728c929ba5b952eb593 Mon Sep 17 00:00:00 2001
From: Gisela Gabernet Garriga <gisela.gabernet@gmail.com>
Date: Mon, 9 Nov 2020 22:41:38 +0100
Subject: [PATCH 1/3] awsbatch config update

---
 conf/awsbatch.config | 14 +++++++++++++-
 docs/awsbatch.md     |  4 +++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/conf/awsbatch.config b/conf/awsbatch.config
index 2e5f83c..43f90db 100644
--- a/conf/awsbatch.config
+++ b/conf/awsbatch.config
@@ -7,7 +7,19 @@ 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'
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.

From 9b5bcbd43436fd086d53790c73202343dbbc58bd Mon Sep 17 00:00:00 2001
From: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Date: Tue, 9 Feb 2021 22:06:59 +0100
Subject: [PATCH 2/3] update aws clipath

---
 conf/awsbatch.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/awsbatch.config b/conf/awsbatch.config
index 43f90db..a8b61b8 100644
--- a/conf/awsbatch.config
+++ b/conf/awsbatch.config
@@ -25,4 +25,4 @@ dag {
 process.executor = 'awsbatch'
 process.queue = params.awsqueue
 aws.region = params.awsregion
-executor.awscli = params.awscli
+aws.batch.cliPath = params.awscli

From 922ab87eb0f69cf994220a4f15f008f9784d16fa Mon Sep 17 00:00:00 2001
From: Asaf Peer <Asaf.Peer@jax.org>
Date: Wed, 24 Mar 2021 11:25:47 -0400
Subject: [PATCH 3/3] added jax singularity cache dir

---
 conf/jax.config | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

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