From 584ddf60b37c1dc8f33b09aa57ba4e56812f540e Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 5 Jan 2024 14:21:31 +0100 Subject: [PATCH 1/3] Revert "Increase time limits" This reverts commit 49cfbd5fc7bb85b41c6219f2bd5b180f2deaa2d8. --- conf/base.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/base.config b/conf/base.config index 77f7a9a5..8c6f6db9 100644 --- a/conf/base.config +++ b/conf/base.config @@ -27,25 +27,25 @@ process { withLabel:process_single { cpus = { check_max( 1 , 'cpus' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 120.h * task.attempt, 'time' ) } + time = { check_max( 8.h * task.attempt, 'time' ) } } withLabel:process_high { cpus = { check_max( 12 * task.attempt, 'cpus' ) } memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 240.h * task.attempt, 'time' ) } + time = { check_max( 16.h * task.attempt, 'time' ) } } withLabel:process_long { - time = { check_max( 240.h * task.attempt, 'time' ) } + time = { check_max( 20.h * task.attempt, 'time' ) } } withLabel:process_high_memory { memory = { check_max( 200.GB * task.attempt, 'memory' ) } From b5bcedbcc6c877d78f6d0ae7dd18fcb42e32c521 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 5 Jan 2024 14:27:36 +0100 Subject: [PATCH 2/3] Move increased runtime limits from base.config to modules.config --- CHANGELOG.md | 2 +- conf/base.config | 4 ---- conf/modules.config | 11 +++++++++++ 3 files changed, 12 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 706c9bfa..a8954815 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update template to v2.11.1 ([#279](https://github.com/nf-core/scrnaseq/pull/279)) - Add support for paired GEX+ATAC sequencing using cellranger-arc ([#274](https://github.com/nf-core/scrnaseq/pull/274)) -- Increase default runtime limits for all processes ([#281])(https://github.com/nf-core/scrnaseq/pull/281) +- Increase default runtime limits for some processes ([#281])(https://github.com/nf-core/scrnaseq/pull/281) - Better support for custom protocols ([#273](https://github.com/nf-core/scrnaseq/pull/273)). - The universc protocol is now specified via the `--protocol` flag - Any protocol specified is now passed to the respective aligner diff --git a/conf/base.config b/conf/base.config index 8c6f6db9..eea930a9 100644 --- a/conf/base.config +++ b/conf/base.config @@ -60,8 +60,4 @@ process { withName:CUSTOM_DUMPSOFTWAREVERSIONS { cache = false } - //Fix for issue 196 - withName: 'NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:ALEVINQC' { - time = '20.h' - } } diff --git a/conf/modules.config b/conf/modules.config index 3bd0631b..5813926a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -17,6 +17,10 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] + withName: FASTQC { + time = { check_max( 120.h * task.attempt, 'time' ) } + } + withName: SAMPLESHEET_CHECK { publishDir = [ path: { "${params.outdir}/pipeline_info" }, @@ -79,6 +83,7 @@ if(params.aligner == "cellranger") { mode: params.publish_dir_mode ] ext.args = {"--chemistry ${meta.chemistry} " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')} + time = { check_max( 240.h * task.attempt, 'time' ) } } } } @@ -105,6 +110,7 @@ if(params.aligner == "cellrangerarc") { mode: params.publish_dir_mode ] ext.args = {meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : ''} + time = { check_max( 240.h * task.attempt, 'time' ) } } } } @@ -134,6 +140,7 @@ if(params.aligner == "universc") { path: "${params.outdir}/universc", mode: params.publish_dir_mode ] + time = { check_max( 240.h * task.attempt, 'time' ) } } } } @@ -159,6 +166,10 @@ if (params.aligner == "alevin") { ] ext.args = "-r cr-like" } + //Fix for issue 196 + withName: 'ALEVINQC' { + time = '120.h' + } } } From bc8825a136c92ff147afe7bbb3095125b99918c6 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 5 Jan 2024 14:29:05 +0100 Subject: [PATCH 3/3] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a8954815..c8cacebb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update template to v2.11.1 ([#279](https://github.com/nf-core/scrnaseq/pull/279)) - Add support for paired GEX+ATAC sequencing using cellranger-arc ([#274](https://github.com/nf-core/scrnaseq/pull/274)) -- Increase default runtime limits for some processes ([#281])(https://github.com/nf-core/scrnaseq/pull/281) +- Increase default runtime limits for some processes ([#281](https://github.com/nf-core/scrnaseq/pull/281), [#284](https://github.com/nf-core/scrnaseq/pull/284)) - Better support for custom protocols ([#273](https://github.com/nf-core/scrnaseq/pull/273)). - The universc protocol is now specified via the `--protocol` flag - Any protocol specified is now passed to the respective aligner