From 670fd3ad7447b673f91e4714aed1c937dd7bd63b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 13 Mar 2019 11:07:55 +0100 Subject: [PATCH 1/4] Add better base config for large ref data (DMGProfiler) --- CHANGELOG.md | 5 +++-- conf/base.config | 1 + 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 72189363c..04923cddd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,11 +9,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Added` ### `Fixed` -* [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171) +* [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171) +* [#153](https://github.com/nf-core/eager/pull/153) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173) ### `Dependencies` -* Added DeDup v0.12.4 (json support) +* Added DeDup v0.12.5 (json support) * Added mtnucratio v0.5 (json support) diff --git a/conf/base.config b/conf/base.config index f5a37ed32..1185f992d 100644 --- a/conf/base.config +++ b/conf/base.config @@ -66,6 +66,7 @@ process { withName: damageprofiler { errorStrategy = 'ignore' + params.large_ref ? "time = { check_max(8.h * task.attempt, 'time') }" : "time = { check_max(2.h * task.attempt, 'time') }" } } From da0b5c2df34ada2c1f4d0468812a0ec79f5c2650 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 13 Mar 2019 11:09:24 +0100 Subject: [PATCH 2/4] Bump Changelog [skip ci] --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 04923cddd..13b5efb6d 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` * [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171) -* [#153](https://github.com/nf-core/eager/pull/153) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173) +* [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173) ### `Dependencies` From 93fdf72d77c61561897d4bd34abafc0e641f2abb Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 19 Mar 2019 14:22:12 +0100 Subject: [PATCH 3/4] Add extra time for bwa index --- conf/base.config | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/base.config b/conf/base.config index 1185f992d..435622d73 100644 --- a/conf/base.config +++ b/conf/base.config @@ -26,14 +26,15 @@ process { memory = { check_max( 2.GB, 'memory' ) } cache = false } - withName:convertBam { cpus = { check_max(8 * task.attempt, 'cpus') } } withName:makeSeqDict { memory = { check_max( 16.GB * task.attempt, 'memory' ) } } - + withname:makeBWAIndex { + time = { check_max(8.h * task.attempt, 'time') } + } withName:bwa { memory = { check_max( 16.GB * task.attempt, 'memory' ) } cpus = { check_max(8 * task.attempt, 'cpus') } From 0b7f7791a1724b4204b0a332291e323f80b01a4b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 4 Apr 2019 14:54:52 +0200 Subject: [PATCH 4/4] Add task defaults for large reference genomes to base config --- conf/base.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 435622d73..a41551062 100644 --- a/conf/base.config +++ b/conf/base.config @@ -33,7 +33,7 @@ process { memory = { check_max( 16.GB * task.attempt, 'memory' ) } } withname:makeBWAIndex { - time = { check_max(8.h * task.attempt, 'time') } + time = params.large_ref ? '12.h' : { check_max(8.h * task.attempt, 'time') } } withName:bwa { memory = { check_max( 16.GB * task.attempt, 'memory' ) }