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..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
@@ -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'
}