From 035156b7711e0a226101557901bb28f85c03fee5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 14 Aug 2018 08:03:47 -0500
Subject: [PATCH] Change to new conventions.
---
workflow/conf/biohpc.config | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index fef1a3f..7d54c2f 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -4,59 +4,59 @@ process {
clusterOptions = '--hold'
// Process specific configuration
- $checkDesignFile {
+ withName: checkDesignFile {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
- $trimReads {
+ withName: trimReads {
module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
cpus = 32
}
- $alignReads{
+ withName: alignReads{
module = ['python/3.6.1-2-anaconda', 'bwa/intel/0.7.12', 'samtools/1.6']
cpus = 32
}
- $filterReads{
+ withName: filterReads{
module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'sambamba/0.6.6', 'bedtools/2.26.0']
cpus = 32
}
- $experimentQC {
+ withName: experimentQC {
module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1']
cpus = 32
}
- $convertReads {
+ withName: convertReads {
module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'bedtools/2.26.0']
cpus = 32
}
- $crossReads {
+ withName: crossReads {
module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2']
cpus = 32
}
- $defineExpDesignFiles {
+ withName: defineExpDesignFiles {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
- $poolAndPsuedoReads {
+ withName: poolAndPsuedoReads {
module = ['python/3.6.1-2-anaconda']
executor = 'local'
}
- $callPeaksMACS {
+ withName: callPeaksMACS {
module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'phantompeakqualtools/1.2', 'UCSC_userApps/v317', 'bedtools/2.26.0']
cpus = 32
}
- $consensusPeaks {
+ withName: consensusPeaks {
module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0']
executor = 'local'
}
- $peakAnnotation {
+ withName: peakAnnotation {
module = ['R/3.4.1-gccmkl']
executor = 'local'
}
- $diffPeaks {
+ withName: diffPeaks {
module = ['R/3.4.1-gccmkl']
cpus = 32
}
- $motifSearch {
+ withName: motifSearch {
module = ['python/2.7.x-anaconda', 'meme/4.11.1-gcc-openmpi', 'bedtools/2.26.0']
cpus = 32
}
--
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