assemblebac-ont - v2.0.3

v2.0.3 - [18/06/2025]

Fixed

• Fix process.shell in nextflow.config (#3416)

- Nextflow
Published by avantonder 8 months ago

assemblebac-ont - v2.0.2

v2.0.2 - [21/03/2025]

Fixed

• Documentation updated
• Flye assembly_info.txt files now included in results

- Nextflow
Published by avantonder 11 months ago

assemblebac-ont - v2.0.1

v2.0.1 - [17/03/2025]

Fixed

• Documentation updated
• DOI generated with Zenodo

- Nextflow
Published by avantonder 11 months ago

assemblebac-ont - v2.0.0.

v2.0.0 - [06/03/2025]

Added

• Significant recoding of pipeline to bring it more in line with current nf-core template
• Python script provided to create new samplesheet format
• Option to QC raw reads using FastQC (default) or Falco added
• Option to use porechop or porechop_abi (default) for adapter removal
• Option to filter reads with nanoq (default) or filtlong
• Falco version 1.2.1 added to pipeline
• FastQC version 0.12.1 added to pipeline
  
• nanoq version 0.10.0 added to pipeline
• Porechop_abi version 0.5.0 added to pipeline

### Fixed

• ARTIC no longer required to create sample list
• Update Bakta from version 1.7.0 to version 1.10.4
• Update Flye from version 2.9 to version 2.9.5
• Update Medaka from version 1.11.3 to version 2.0.1
• Medaka model files are now pulled from the Medaka Github page
• Update mlst from version 2.19.0 to version 2.23.0
• Update MultiQC from version 1.14 to version 1.25.1
• Documentation updated

- Nextflow
Published by avantonder 12 months ago

assemblebac-ont - v1.1.1.

v1.1.1 - [08/02/2023]

Added

-Update Medaka to version 1.11.3

- Nextflow
Published by avantonder about 2 years ago

assemblebac-ont - v1.1

v1.1 - [23/01/2023]

Added

• Parse Flye output logs to produce flye_stats.tsv summary file in metadata directory
• Save Flye .gfa.gz assembly graph files in flye directory
• List Flye data options in parameters.md

Fixed

• Rename --subsampling_off to --skip_subsampling
• Corrected ARCTIC to ARTIC in metromap figure

- Nextflow
Published by avantonder about 2 years ago

assemblebac-ont - v1.0.0

v1.0.0 - [20/09/2023]

Initial release of avantonder/assembleBAC-ONT, created with the nf-core template.

- Nextflow
Published by avantonder over 2 years ago