Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bump version 2.2.0dev #100

Merged
merged 3 commits into from
Oct 24, 2023
Merged

Bump version 2.2.0dev #100

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
cca4d5c
bump version to 2.2.0dev
Daniel-VM Oct 23, 2023
97c8afe
fix indentation in mainfest
Daniel-VM Oct 24, 2023
8a24a5a
update formatting in comments of allowed options
Daniel-VM Oct 24, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 12 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/2.1.0" target="_blank">nf-core/bacass</a>
This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/dev" target="_blank">nf-core/bacass</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/bacass/2.1.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/bacass/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-bacass-methods-description":
order: -1000
Expand Down
14 changes: 7 additions & 7 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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'
}

Expand Down