From b9b8899e9642d6ed841b8b653bd9fe18b557bbb3 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Mon, 27 May 2024 11:38:35 +0200 Subject: [PATCH 1/3] Supply memory to Megahit --- modules/local/megahit/interleaved.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/megahit/interleaved.nf b/modules/local/megahit/interleaved.nf index 4c940320..79c4d1dd 100644 --- a/modules/local/megahit/interleaved.nf +++ b/modules/local/megahit/interleaved.nf @@ -39,6 +39,7 @@ process MEGAHIT_INTERLEAVED { pigz \\ --no-name \\ -p $task.cpus \\ + -m ${task.memory.toBytes()} \\ $args2 \\ megahit_out/*.fa \\ megahit_out/intermediate_contigs/*.fa From 326637836e2810bd2f388d8190033a54f4048b92 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Mon, 27 May 2024 11:40:44 +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 c5cd384e..a3371d29 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co ### `Changed` +- [#292](<[https://github.com/nf-core/metatdenovo/pull/292](https://github.com/nf-core/metatdenovo/pull/292)>) - Specify memory to Megahit process - [#290](<[https://github.com/nf-core/metatdenovo/pull/290](https://github.com/nf-core/metatdenovo/pull/290)>) - Template update to v2.14.1 - [#283](<[https://github.com/nf-core/metatdenovo/pull/283](https://github.com/nf-core/metatdenovo/pull/283)>) - Updated documentation about download databases manually - [#268](<[https://github.com/nf-core/metatdenovo/pull/268](https://github.com/nf-core/metatdenovo/pull/268)>) - Don't save so many intermediate Megahit files by default From 57a94d6900c8c774e9b1dc7c609cc262837d4ebe Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Mon, 27 May 2024 11:49:09 +0200 Subject: [PATCH 3/3] Specified memory for the wrong program --- modules/local/megahit/interleaved.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/megahit/interleaved.nf b/modules/local/megahit/interleaved.nf index 79c4d1dd..93d801fb 100644 --- a/modules/local/megahit/interleaved.nf +++ b/modules/local/megahit/interleaved.nf @@ -33,13 +33,13 @@ process MEGAHIT_INTERLEAVED { $pair_ends \\ ${single_ends} \\ -t $task.cpus \\ + -m ${task.memory.toBytes()} \\ $args \\ --out-prefix $assembly pigz \\ --no-name \\ -p $task.cpus \\ - -m ${task.memory.toBytes()} \\ $args2 \\ megahit_out/*.fa \\ megahit_out/intermediate_contigs/*.fa