From 09cb56b3615cdec244743d931824f4da1d46639d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 21 Feb 2020 11:32:50 -0600
Subject: [PATCH] Fix nextflow config layering problem
---
workflow/conf/aws.config | 4 ++++
workflow/conf/aws_ondemand.config | 9 ---------
workflow/conf/aws_spot.config | 9 ---------
workflow/conf/aws_user.config | 9 ---------
workflow/conf/biohpc.config | 24 ------------------------
workflow/conf/biohpc_cluster.config | 7 +++++++
workflow/conf/biohpc_local.config | 22 ++++++++++++++++++++++
workflow/nextflow.config | 9 ---------
8 files changed, 33 insertions(+), 60 deletions(-)
delete mode 100755 workflow/conf/aws_ondemand.config
delete mode 100755 workflow/conf/aws_spot.config
delete mode 100644 workflow/conf/aws_user.config
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index 7794329..6875c65 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -1,11 +1,15 @@
+workDir = 's3://'
aws.client.storageEncryption = 'AES256'
aws {
+ region = ''
batch {
cliPath = '/home/ec2-user/miniconda/bin/aws'
}
}
process {
+ executor = 'awsbatch'
+ queue = 'default-'
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
deleted file mode 100755
index d12c2de..0000000
--- a/workflow/conf/aws_ondemand.config
+++ /dev/null
@@ -1,9 +0,0 @@
-workDir = 's3://
-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
deleted file mode 100755
index 0a81a79..0000000
--- a/workflow/conf/aws_spot.config
+++ /dev/null
@@ -1,9 +0,0 @@
-workDir = 's3://'
-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
deleted file mode 100644
index 68dd2f5..0000000
--- a/workflow/conf/aws_user.config
+++ /dev/null
@@ -1,9 +0,0 @@
-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 eb1fc5c..bdcc3c4 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -1,27 +1,3 @@
-process {
- withLabel: checkDesignFile {
- module = ['python/3.6.1-2-anaconda']
- }
- withLabel: count211 {
- module = ['cellranger/2.1.1']
- }
- withLabel: count301 {
- module = ['cellranger/3.0.1']
- }
- withLabel: count302 {
- module = ['cellranger/3.0.2']
- }
- withLabel: count310 {
- module = ['cellranger/3.1.0']
- }
- withLabel: versions {
- module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
- }
- withLabel: multiqc {
- module = ['multiqc/1.7']
- }
-}
-
params {
// Reference file paths on BioHPC
genomes {
diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config
index 789d1e9..bebd64a 100644
--- a/workflow/conf/biohpc_cluster.config
+++ b/workflow/conf/biohpc_cluster.config
@@ -4,24 +4,31 @@ process {
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'
}
}
\ No newline at end of file
diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc_local.config
index 9ca703b..0eb72d4 100755
--- a/workflow/conf/biohpc_local.config
+++ b/workflow/conf/biohpc_local.config
@@ -1,3 +1,25 @@
process {
executor = 'local'
+
+ withLabel: checkDesignFile {
+ module = ['python/3.6.1-2-anaconda']
+ }
+ withLabel: count211 {
+ module = ['cellranger/2.1.1']
+ }
+ withLabel: count301 {
+ module = ['cellranger/3.0.1']
+ }
+ withLabel: count302 {
+ module = ['cellranger/3.0.2']
+ }
+ withLabel: count310 {
+ module = ['cellranger/3.1.0']
+ }
+ withLabel: versions {
+ module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+ }
+ withLabel: multiqc {
+ module = ['multiqc/1.7']
+ }
}
\ No newline at end of file
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index f1a8650..9496393 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -11,15 +11,6 @@ profiles {
aws {
includeConfig 'conf/aws.config'
}
- ondemand {
- includeConfig 'conf/aws_ondemand.config'
- }
- spot {
- includeConfig 'conf/aws_spot.config'
- }
- awsUserDefined {
- includeConfig 'conf/aws_user.config'
- }
}
trace {
--
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