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 -- GitLab