From 672467a60752e4fd8cdd704e87105e2cc08d3c3f Mon Sep 17 00:00:00 2001 From: Konrad Rokicki Date: Wed, 22 Nov 2023 13:27:22 -0500 Subject: [PATCH 1/2] fixed "protection stack overflow" issue by setting max-ppsize --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index 995f95e1..7f923394 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -418,6 +418,7 @@ process { } withName: 'PHANTOMPEAKQUALTOOLS' { + ext.args = { "--max-ppsize=500000" } ext.args2 = { "-p=$task.cpus" } publishDir = [ path: { "${params.outdir}/${params.aligner}/merged_library/phantompeakqualtools" }, From 0bb54eb148f411a07b3789a22d1b69b20fb63c81 Mon Sep 17 00:00:00 2001 From: Konrad Rokicki Date: Wed, 22 Nov 2023 13:39:49 -0500 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 949a35c8..b936b306 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#343](https://github.com/nf-core/chipseq/issues/343)] - Provide replicate information explicitly in samplesheet. - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10). - [[#367](https://github.com/nf-core/chipseq/issues/367)] - Get rid of `CheckIfExists` for params paths. +- [[#370](https://github.com/nf-core/chipseq/issues/370)] - Fix stack overflow exceptions in phantompeakqualtools ([see here](https://github.com/kundajelab/phantompeakqualtools/issues/3)). ### Software dependencies