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.
Changed
- #86 - Update nf-core/bacass to the new nf-core 2.9
TEMPLATE.
- #61 - Update local/modules to nf-core/modules (detailed below).
- #91 - Update nf-core/bacass to the new nf-core 2.10
TEMPLATE.
- #95 - Update MultiQC module to v1.17.
Added
- #86 - Added nf-core subworkflow for trimming and QC of short-reads nf-core/fastq_trim_fastp_fastqc.
- #88 - Added nf-validation on samplesheet
- #93 - Added missing modules output to MultiQC. ( Fastp, PycoQC, Porechop, Quast, Kraken2, and Prokka).
- #95 - Added subworkflow for gene annotation with Bakta.
Fixed
- Fixed modules
- Medaka: Medaka last version (see version update below) doesn't allow gzip compressed files. Add bgzip compression instead.
- Dfast: fix overwriting issues detected when copying sample files from
work/ to results/
Dependencies
- #61 - Update local/modules to nf-core/modules plus version update.
| Tool |
Previous version |
New version |
| Canu |
2.1.1 |
2.2 |
| Minimap2 |
2.21 |
2.2 |
| Miniasm |
0.3 |
- |
| Racon |
1.4.20-1 |
- |
- Update already nf-core modules
| Tool |
Previous version |
New version |
| Fastqc |
0.11.9 |
- |
| Samtools |
1.13 |
2.1.2 |
| Kraken2 |
2.1.1 |
2.1.2 |
| Quast |
5.0.2 |
5.2.0 |
| Prokka |
1.14.6 |
- |
| Multiqc |
1.10.1 |
1.15 |
- Refactor
local/modules making them follow nf-core v2.9 structure/fashion.
| Tool |
Previous version |
New version |
| Dfast |
1.2.14 |
- |
| Medaka |
1.4.3-0 |
- |
| Nanoplot |
1.38.0 |
1.41.6 |
| Nanopolish |
0.13.2-5 |
0.14.0 |
| Pycoqc |
2.5.2 |
- |
| Unicycler |
0.4.8 |
- |
Deprecated
