From cca4d5cc3d26e45dcdf755696c5fe7ece380217f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 23 Oct 2023 14:02:13 +0200 Subject: [PATCH 1/3] bump version to 2.2.0dev --- CHANGELOG.md | 12 ++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9d3b4376..27b027f0 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). +## v2.2.0dev nf-core/bacass: "Aqua Platinum Zebrafish" + +### `Changed` + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v2.1.0 nf-core/bacass: "Navy Steel Swordfish" - 2023/10/20 This version merges the nf-core template updates of v2.9 and v2.10, and updates modules or dependencies to ensure compatibility with the new template. Additionally, new modules have been added to process short-reads and perform gene annotation with Bakta. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d0641e6a..d1c68735 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/bacass + This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-bacass-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 66e2cced..4d9e6107 100644 --- a/nextflow.config +++ b/nextflow.config @@ -255,7 +255,7 @@ manifest { description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.1.0' + version = '2.2.0dev' doi = '10.5281/zenodo.2669428' } From 97c8afe9e26c5271e5f6dce3476ec24bc39e9cdf Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 24 Oct 2023 09:04:11 +0200 Subject: [PATCH 2/3] fix indentation in mainfest --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 4d9e6107..9deef23f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -255,7 +255,7 @@ manifest { description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2.0dev' + version = '2.2.0dev' doi = '10.5281/zenodo.2669428' } From 8a24a5ac70f878d4e8c0f0af0dadf558e108047f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 24 Oct 2023 10:26:18 +0200 Subject: [PATCH 3/3] update formatting in comments of allowed options --- nextflow.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/nextflow.config b/nextflow.config index 9deef23f..48520b15 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,21 +20,21 @@ params { kraken2db = "" // Assembly parameters - assembler = 'unicycler' //allowed are unicycler, canu, miniasm - assembly_type = 'short' //allowed are short, long, hybrid (hybrid works only with Unicycler) + assembler = 'unicycler' // Allowed: ['unicycler', 'canu', 'miniasm'] + assembly_type = 'short' // Allowed: ['short', 'long', 'hybrid'] (hybrid works only with Unicycler) unicycler_args = "" - canu_mode = '-nanopore' // allowed modes: ["-pacbio", "-nanopore", "-pacbio-hifi"] - canu_args = '' //Default no extra options, can be adjusted by the user + canu_mode = '-nanopore' // Allowed: ['-pacbio', '-nanopore', '-pacbio-hifi'] + canu_args = '' // Default no extra options, can be adjusted by the user // Assembly polishing polish_method = 'medaka' // Annotation - annotation_tool = 'prokka' // allowed are 'prokka', 'bakta' or 'dfast' + annotation_tool = 'prokka' // Allowed: ['prokka', 'bakta','dfast'] prokka_args = "" baktadb = '' baktadb_download = false - baktadb_download_args = '--type light' // allowed: '--type light' or '--type full' + baktadb_download_args = '--type light' // Allowed: ['--type light', '--type full'] dfast_config = "$projectDir/assets/test_config_dfast.py" // Skipping options