From d52002e7a34cd43a8465bfd0fdff8d64addb5d47 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Apr 2022 13:50:59 +0200 Subject: [PATCH 1/3] Fix raw FASTQC single-end threads --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index ae21a644e..3ed1e2f3d 100644 --- a/main.nf +++ b/main.nf @@ -703,7 +703,7 @@ process fastqc { """ } else { """ - fastqc -q $r1 + fastqc -t ${task.cpus} -q $r1 rename 's/_fastqc\\.zip\$/_raw_fastqc.zip/' *_fastqc.zip rename 's/_fastqc\\.html\$/_raw_fastqc.html/' *_fastqc.html """ From 44b115ff38b75730c33659b637501cf57bd4d6bb Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Apr 2022 13:52:43 +0200 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c71a07822..b89f37637 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian) +- [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter to pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting) ### `Dependencies` From bec759fb87a15f93290ace2d10376c480902150a Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Apr 2022 13:55:07 +0200 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b89f37637..a9a23c86b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian) -- [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter to pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting) +- [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting) ### `Dependencies`