From 5fbdda42d3ff5249586e9d2eec1c79fd5e9061cb Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sun, 27 Oct 2024 16:14:02 +0100 Subject: [PATCH 1/7] Post 3.2.0 release version bump --- .nf-core.yml | 2 +- CHANGELOG.md | 12 ++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 4 files changed, 16 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 5d193256..558d7eee 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,5 +18,5 @@ template: org: nf-core outdir: . skip_features: null - version: 3.2.0 + version: 3.3.0dev update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index 43c68211..a902cd7b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ 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). +## dev [unreleased] + +### `Added` + +### `Changed` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## 3.2.0 [2024-10-27] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e9da7a41..fe8d388f 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/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 026f67d8..07325acf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.2.0' + version = '3.3.0dev' doi = '10.1093/nargab/lqac007' } From 0149ed214db563b40e12db84845a065c19bde56b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 29 Oct 2024 14:02:44 +0000 Subject: [PATCH 2/7] Prepare for patch --- .nf-core.yml | 2 +- CHANGELOG.md | 2 ++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 558d7eee..5e2971cf 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,5 +18,5 @@ template: org: nf-core outdir: . skip_features: null - version: 3.3.0dev + version: 3.0.1 update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index a902cd7b..0156701b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#707](https://github.com/nf-core/mag/pull/674) - Fix missing space resulting in malformed args for MEGAHIT (reported by @d4straub, fix by @jfy133) + ### `Dependencies` ### `Deprecated` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index fe8d388f..434dfa7b 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/mag + This report has been generated by the nf-core/mag analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mag-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 07325acf..4c5e67fa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -375,7 +375,7 @@ manifest { description = """Assembly, binning and annotation of metagenomes""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.3.0dev' + version = '3.2.1' doi = '10.1093/nargab/lqac007' } From 229197447c910cc19fe5ad411e454562b582ed07 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 29 Oct 2024 14:05:08 +0000 Subject: [PATCH 3/7] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0156701b..8296e383 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## dev [unreleased] +## 3.2.1 [2024-10-29] ### `Added` From dbe49fe704e3f0baaa5c60e198ebd8ba268d2b06 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 29 Oct 2024 15:05:54 +0100 Subject: [PATCH 4/7] Add sapces to MEGAHIT options to stop breaking args list --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 0fbea292..d6ee1d73 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -257,7 +257,7 @@ process { } withName: MEGAHIT { - ext.args = { params.megahit_options ? params.megahit_options + "-m ${task.memory.toBytes()}" : "-m ${task.memory.toBytes()}" } + ext.args = { params.megahit_options ? params.megahit_options + " -m ${task.memory.toBytes()}" : " -m ${task.memory.toBytes()}" } ext.prefix = { "MEGAHIT-${meta.id}" } publishDir = [path: { "${params.outdir}/Assembly/MEGAHIT" }, mode: params.publish_dir_mode, pattern: "*.{fa.gz,log}"] } From 4c43894c156d77d04bfd2f73c220ef795463a947 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 29 Oct 2024 15:06:40 +0100 Subject: [PATCH 5/7] Update .nf-core.yml --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 5e2971cf..f945d00c 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,5 +18,5 @@ template: org: nf-core outdir: . skip_features: null - version: 3.0.1 + version: 3.2.1 update: null From 52ccb1cdf4e4d4861a4521b51da3c6f6acec84ba Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 29 Oct 2024 15:53:58 +0100 Subject: [PATCH 6/7] Update modules.config --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index d6ee1d73..507e475f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -257,7 +257,7 @@ process { } withName: MEGAHIT { - ext.args = { params.megahit_options ? params.megahit_options + " -m ${task.memory.toBytes()}" : " -m ${task.memory.toBytes()}" } + ext.args = { params.megahit_options ? params.megahit_options + " -m ${task.memory.toBytes()}" : "-m ${task.memory.toBytes()}" } ext.prefix = { "MEGAHIT-${meta.id}" } publishDir = [path: { "${params.outdir}/Assembly/MEGAHIT" }, mode: params.publish_dir_mode, pattern: "*.{fa.gz,log}"] } From daa493f46ebcee8f25d1cb25307d59b9564b2aaf Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 30 Oct 2024 10:15:41 +0100 Subject: [PATCH 7/7] Apply suggestions from code review --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8296e383..f7b929e3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## 3.2.1 [2024-10-29] +## 3.2.1 [2024-10-30] ### `Added`