From 45a764cc00fdc75bc6e67baf4d8d5542ad9c0747 Mon Sep 17 00:00:00 2001 From: d4straub Date: Wed, 13 Nov 2024 11:37:05 +0100 Subject: [PATCH 1/4] bump version 2.12.0 --- .nf-core.yml | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index db3cd2f0..85c8915d 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -23,7 +23,7 @@ template: outdir: . skip_features: - igenomes - version: 2.12.0dev + version: 2.12.0 update: https://github.com/nf-core/modules.git: nf-core: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a363d72d..699ea0f7 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/ampliseq + This report has been generated by the nf-core/ampliseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-ampliseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3894f9fb..4fb664b5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -346,7 +346,7 @@ manifest { description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '2.12.0dev' + version = '2.12.0' doi = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420' } From 96be42b0bd5f3e7bbc058f52bd94af80ea8b3b9a Mon Sep 17 00:00:00 2001 From: d4straub Date: Wed, 13 Nov 2024 11:39:32 +0100 Subject: [PATCH 2/4] update CHANGELOG --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index af0c4239..06384802 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). -## nf-core/ampliseq version 2.12.0dev +## nf-core/ampliseq version 2.12.0 ### `Added` @@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#785](https://github.com/nf-core/ampliseq/pull/785) - Template update for nf-core/tools version 3.0.2 +- [#785](https://github.com/nf-core/ampliseq/pull/785),[#795](https://github.com/nf-core/ampliseq/pull/795) - Template update for nf-core/tools version 3.0.2 - [#786](https://github.com/nf-core/ampliseq/pull/786) - Creation of the summary report was failing with `--dada_ref_taxonomy silva=132` - [#792](https://github.com/nf-core/ampliseq/pull/792) - Remove white spaces in process tags to avoid errors on some systems From 0052ee05845b7840976f9b106a9904c85fbe0876 Mon Sep 17 00:00:00 2001 From: d4straub Date: Wed, 13 Nov 2024 12:22:19 +0100 Subject: [PATCH 3/4] include custom configs --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 4fb664b5..97d006e7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -286,7 +286,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load nf-core/ampliseq custom profiles from different institutions. // nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/ampliseq.config" : "/dev/null" +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/ampliseq.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled From 88b5322c8f977a5cca7321c959c149727f79d611 Mon Sep 17 00:00:00 2001 From: d4straub Date: Wed, 13 Nov 2024 12:26:11 +0100 Subject: [PATCH 4/4] update docs --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 0ca85af0..3a340800 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -323,7 +323,7 @@ nextflow pull nf-core/ampliseq It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/ampliseq releases page](https://github.com/nf-core/ampliseq/releases) and find the latest pipeline version - numeric only (eg. `2.4.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.4.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [nf-core/ampliseq releases page](https://github.com/nf-core/ampliseq/releases) and find the latest pipeline version - numeric only (eg. `2.12.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.12.0`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.