From 5b7441bc597a60dec5e07331487b2b8e28806023 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Nov 2023 16:22:42 +0000 Subject: [PATCH 1/5] bump versions --- CHANGELOG.md | 9 +++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e080218d..6b4bbad1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.5.0dev + +### `Added` + +### `Fixed` + +### `Changed` + + ## v1.4.0 - 2023-11-27 ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f921df86..211358cb 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/differentialabundance + This report has been generated by the nf-core/differentialabundance analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-differentialabundance-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 5c678174..f1531748 100644 --- a/nextflow.config +++ b/nextflow.config @@ -386,7 +386,7 @@ manifest { description = 'Differential abundance analysis' mainScript = 'main.nf' nextflowVersion = '!>=23.10.0' - version = '1.4.0' + version = '1.5.0dev' doi = '10.5281/zenodo.7568000' } From c0c4de63b25b7422dfbbbce1f1e3595e2046c0de Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Nov 2023 16:25:04 +0000 Subject: [PATCH 2/5] Fix resource issues --- conf/base.config | 2 +- modules.json | 4 ++-- modules/nf-core/deseq2/differential/main.nf | 2 +- modules/nf-core/limma/differential/main.nf | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/base.config b/conf/base.config index cbc9311c..59ef2e92 100644 --- a/conf/base.config +++ b/conf/base.config @@ -36,7 +36,7 @@ process { } withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 2.GB * task.attempt, 'memory' ) } + memory = { check_max( 36.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } withLabel:process_high { diff --git a/modules.json b/modules.json index e2f69a77..f65a0b01 100644 --- a/modules.json +++ b/modules.json @@ -37,7 +37,7 @@ }, "deseq2/differential": { "branch": "master", - "git_sha": "c992bd93b22a97feda5f04755511366c45423626", + "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", "installed_by": ["modules"] }, "geoquery/getgeo": { @@ -57,7 +57,7 @@ }, "limma/differential": { "branch": "master", - "git_sha": "25047aa940979f64b31d19b94c483a9254263892", + "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", "installed_by": ["modules"] }, "proteus/readproteingroups": { diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf index 3c797f7b..ab7bc06a 100644 --- a/modules/nf-core/deseq2/differential/main.nf +++ b/modules/nf-core/deseq2/differential/main.nf @@ -1,6 +1,6 @@ process DESEQ2_DIFFERENTIAL { tag "$meta" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf index 56e02950..384e4649 100644 --- a/modules/nf-core/limma/differential/main.nf +++ b/modules/nf-core/limma/differential/main.nf @@ -1,6 +1,6 @@ process LIMMA_DIFFERENTIAL { tag "$meta" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From c993eac3b78034e2a33f8ba8c8c53aa376516073 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Nov 2023 16:26:47 +0000 Subject: [PATCH 3/5] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b4bbad1..f5352240 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [[#208](https://github.com/nf-core/differentialabundance/pull/208)] - Fix resource issues and bump versions ([@pinin4fjords](https://github.com/pinin4fjords), review by ) + ### `Changed` From 2b2caae55a50dc6646178ff2f3d53507a3015092 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 27 Nov 2023 16:28:43 +0000 Subject: [PATCH 4/5] [automated] Fix linting with Prettier --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f5352240..a1c43515 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - ## v1.4.0 - 2023-11-27 ### `Added` From 3f56135982c8a7503892a208728ac89cdb280da6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Nov 2023 16:44:52 +0000 Subject: [PATCH 5/5] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f5352240..eb6c87af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [[#208](https://github.com/nf-core/differentialabundance/pull/208)] - Fix resource issues and bump versions ([@pinin4fjords](https://github.com/pinin4fjords), review by ) +- [[#208](https://github.com/nf-core/differentialabundance/pull/208)] - Fix resource issues and bump versions ([@pinin4fjords](https://github.com/pinin4fjords), review by [@sguizard](https://github.com/sguizard)) ### `Changed`