Simple bacterial assembly and annotation pipeline
Changed
Added
Fixed
Dependencies
Tool | Previous version | New version |
---|---|---|
Bakta | 1.8.2 | 1.9.3 |
Canu | 2.2 | - |
Dragonflye | 1.1.2 | - |
Fastp | 0.23.4 | - |
Kraken2 | 2.1.2 | - |
Miniasm | 0.3_r179 | - |
Minimap2 | 2.2 | 2.24 |
Nanoplot | 1.41.6 | - |
Porechop | 0.2.4 | - |
Prokka | 1.14.6 | - |
Quast | 5.2.0 | - |
Racon | 1.4.20 | - |
Samtools | 1.17 | 1.19.2 |
Untar | 1.34 | - |
Dfast | 1.2.20 | - |
Medaka | 1.4.3-0 | - |
Nanopolish | 0.14.0 | - |
PycoQC | 2.5.2 | - |
Unicycler | 0.4.8 | - |
Deprecated
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
TEMPLATE
.TEMPLATE
.Added
Fixed
work/
to results/
Dependencies
Tool | Previous version | New version |
---|---|---|
Canu | 2.1.1 | 2.2 |
Minimap2 | 2.21 | 2.2 |
Miniasm | 0.3 | - |
Racon | 1.4.20-1 | - |
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 |
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
#86 Replace depecated modules with nf-core/modules.
local/get_software_versions.nf
with nf-core/custom/dumpsoftwareversions.nf
local/skewer
by nf-core/fastp
and wrap fastqc plus fastp into subworkflows/nf-core/fastq_trim_fastp_fastqc
Main changes are conversion from nextflow DSL1 to DSL2. Additionally, the template and software was updated, as detailed below.
Changed
TEMPLATE
--krakendb
now expects a .tar.gz
/.tgz
(compressed tar archive) directly from https://benlangmead.github.io/aws-indexes/k2
instead of an uncompressed folder.Added
Fixed
Dependencies
This is basically a maintenance update that includes template updates, fixed environments and some minor bugfixes.
Merged in nf-core/tools template v 1.11
Updated multiple dependencies:
Switched out containers for many tools to make DSLv2 transition easier (escape from dependency hell)
Initial release of nf-core/bacass, created with the nf-core template.
This pipeline is for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using Skewer and performs basic QC using FastQC. Afterwards, the pipeline performs read assembly using Unicycler and assesses assembly quality using QUAST. Contamination of the assembly is checked using Kraken2 to verify sample purity. The resulting bacterial assembly is annotated using Prokka.
Furthermore, the pipeline creates various reports in the results directory specified, including a MultiQC report summarizing some of the findings and software versions.