From dee481129bd69c13236db471603e9a18d6739826 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 28 Jul 2020 18:36:23 -0500
Subject: [PATCH] Update configuration for queue to fix large number of reads.
---
CHANGELOG.md | 1 +
workflow/main.nf | 5 +++++
2 files changed, 6 insertions(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c577672..f246498 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ All notable changes to this project will be documented in this file.
## [Unreleased ]
### Upgraded
- Updated support for astrocyte 0.3.1
+- Added queue information to fix memory issue
## [publish_2.0.3 ] - 2020-06-21
### Fixed
diff --git a/workflow/main.nf b/workflow/main.nf
index aee4aa5..d904b5e 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -213,6 +213,7 @@ process alignReads {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}/${sampleId}", mode: 'copy'
+ queue '256GB,256GBv1'
input:
set sampleId, reads, experimentId, replicate, fqLength from trimmedReads
@@ -264,6 +265,7 @@ process filterReads {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}/${sampleId}", mode: 'copy'
+ queue '128GB,256GB,256GBv1'
input:
set sampleId, mapped, experimentId, replicate from mappedReads
@@ -326,6 +328,7 @@ process convertReads {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}", mode: 'copy'
+ queue '128GB,256GB,256GBv1'
input:
set sampleId, deduped, bai, experimentId, replicate from convertReads
@@ -501,6 +504,7 @@ process callPeaksMACS {
tag "${sampleId}-${replicate}"
publishDir "${outDir}/${task.process}/${experimentId}/${replicate}", mode: 'copy'
+ queue '128GB,256GB,256GBv1'
input:
set sampleId, tagAlign, xcor, experimentId, replicate from experimentRows
@@ -638,6 +642,7 @@ process peakAnnotation {
process experimentQC {
publishDir "${outDir}/${task.process}", mode: 'copy'
+ queue '128GB,256GB,256GBv1'
input:
file designExperimentQC
--
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