From 6669d2a9dddbe14b8c4b613b05d3d1ec747a9629 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 21 Feb 2020 10:56:13 -0600
Subject: [PATCH] Add config update (layered)
---
workflow/conf/aws.config | 11 ++++++++++
workflow/conf/aws_ondemand.config | 9 ++++++++
workflow/conf/aws_spot.config | 9 ++++++++
workflow/conf/aws_user.config | 9 ++++++++
workflow/conf/biohpc.config | 34 +----------------------------
workflow/conf/biohpc_cluster.config | 27 +++++++++++++++++++++++
workflow/conf/biohpc_local.config | 3 +++
7 files changed, 69 insertions(+), 33 deletions(-)
create mode 100644 workflow/conf/aws.config
create mode 100755 workflow/conf/aws_ondemand.config
create mode 100755 workflow/conf/aws_spot.config
create mode 100644 workflow/conf/aws_user.config
create mode 100644 workflow/conf/biohpc_cluster.config
create mode 100755 workflow/conf/biohpc_local.config
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
new file mode 100644
index 0000000..7794329
--- /dev/null
+++ b/workflow/conf/aws.config
@@ -0,0 +1,11 @@
+aws.client.storageEncryption = 'AES256'
+aws {
+ batch {
+ cliPath = '/home/ec2-user/miniconda/bin/aws'
+ }
+}
+
+process {
+ cpus = 1
+ memory = '10 GB'
+}
\ No newline at end of file
diff --git a/workflow/conf/aws_ondemand.config b/workflow/conf/aws_ondemand.config
new file mode 100755
index 0000000..d07f84a
--- /dev/null
+++ b/workflow/conf/aws_ondemand.config
@@ -0,0 +1,9 @@
+workDir = 's3://gudmap.rbk/work'
+aws {
+ region = 'us-east-2'
+}
+
+process {
+ executor = 'awsbatch'
+ queue = 'highpriority-'
+}
\ No newline at end of file
diff --git a/workflow/conf/aws_spot.config b/workflow/conf/aws_spot.config
new file mode 100755
index 0000000..4928b22
--- /dev/null
+++ b/workflow/conf/aws_spot.config
@@ -0,0 +1,9 @@
+workDir = 's3://gudmap.rbk/work'
+aws {
+ region = 'us-east-2'
+}
+
+process {
+ executor = 'awsbatch'
+ queue = 'default-'
+}
\ No newline at end of file
diff --git a/workflow/conf/aws_user.config b/workflow/conf/aws_user.config
new file mode 100644
index 0000000..68dd2f5
--- /dev/null
+++ b/workflow/conf/aws_user.config
@@ -0,0 +1,9 @@
+workDir = 's3://'
+aws {
+ region = ''
+}
+
+process {
+ executor = 'awsbatch'
+ queue = ''
+}
\ No newline at end of file
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 0972a89..eb1fc5c 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -1,35 +1,24 @@
process {
- executor = 'slurm'
- queue = 'super'
- clusterOptions = '--hold'
-
withLabel: checkDesignFile {
module = ['python/3.6.1-2-anaconda']
- executor = 'local'
}
withLabel: count211 {
module = ['cellranger/2.1.1']
- queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count301 {
module = ['cellranger/3.0.1']
- queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count302 {
module = ['cellranger/3.0.2']
- queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count310 {
module = ['cellranger/3.1.0']
- queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: versions {
module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
- executor = 'local'
}
withLabel: multiqc {
module = ['multiqc/1.7']
- executor = 'local'
}
}
@@ -82,25 +71,4 @@ params {
param = 'SC3Pv3'
}
}
-}
-
-trace {
- enabled = true
- file = 'pipeline_trace.txt'
- fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
-}
-
-timeline {
- enabled = true
- file = 'timeline.html'
-}
-
-report {
- enabled = true
- file = 'report.html'
-}
-
-tower {
- accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
- enabled = true
-}
+}
\ No newline at end of file
diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config
new file mode 100644
index 0000000..789d1e9
--- /dev/null
+++ b/workflow/conf/biohpc_cluster.config
@@ -0,0 +1,27 @@
+process {
+ executor = 'slurm'
+ queue = 'super'
+ clusterOptions = '--hold'
+
+ withLabel: checkDesignFile {
+ executor = 'local'
+ }
+ withLabel: count211 {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count301 {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count302 {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count310 {
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: versions {
+ executor = 'local'
+ }
+ withLabel: multiqc {
+ executor = 'local'
+ }
+}
\ No newline at end of file
diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc_local.config
new file mode 100755
index 0000000..9ca703b
--- /dev/null
+++ b/workflow/conf/biohpc_local.config
@@ -0,0 +1,3 @@
+process {
+ executor = 'local'
+}
\ No newline at end of file
--
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