Main changes are conversion from nextflow DSL1 to DSL2. Additionally, the template and software was updated, as detailed below.

Changed

• #56 - Switched to DSL2 & update to new nf-core 2.1 TEMPLATE
• #56 - --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

• #56 - Added full size test dataset, two Zetaproteobacteria sequenced with Illumina MiSeq Reagent Kit V2, PE250, 3 to 4 million read pairs.

Fixed

• #51 - Fixed Unicycler

Dependencies

• #56 - Updated a bunch of dependencies (unchanged: FastQC, Miniasm, Prokka, Porechop, QUAST)
  • Unicycler from 0.4.4 to 0.4.8
  • Kraken2 from 2.0.9beta to 2.1.1
  • MultiQC from 1.9 to 1.10.1
  • PYCOQC from 2.5.0.23 to 2.5.2
  • Samtools from 1.11 to 1.13
  • Canu from 2.0 to 2.1.1-2
  • dfast from 1.2.10 to 1.2.14
  • Medaka from 1.1.2 to 1.4.3-0
  • Minimap 2 from 2.17 to 2.21
  • Nanoplot from 1.32.1 to 1.38.0
  • Nanopolish from 0.13.2 to 0.13.2-5
  • Racon from 1.4.13 to 1.4.20-1
  • Skewer from 0.2.2 to 0.2.2-3

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:

  • fastqc=0.11.8, 0.11.9 multiqc=1.8, 1.9 kraken2=2.0.8_beta, 2.0.9beta prokka=1.14.5, 1.14.6 nanopolish=0.11.2, 0.13.2 parallel=20191122, 20200922 racon=1.4.10, 1.4.13 canu=1.9, 2.0 samtools=1.9, 1.11 nanoplot=1.28.1, 1.32.1 pycoqc=2.5.0.3, 2.5.0.23

• Switched out containers for many tools to make DSLv2 transition easier (escape from dependency hell)

v1.1.0 nf-core/bacass: “Green Aluminium Shark” 2019/12/13

• Added support for hybrid assembly using Nanopore and Illumina Short Reads
• Added methods for long-read Nanopore data
  • Nanopolish, for polishing of Nanopore data with Illumina reads
  • Medaka, as alternative assembly polishing method
  • PoreChop, for quality trimming of Nanopore data
  • Nanoplot, for plotting quality metrics of Nanopore data
  • PycoQC, to QC Nanopore data
• Added multiple tools to assemble long-reads
  • Miniasm + Racon
  • Canu Assembler
  • Unicycler in Long read Mode
• Add alternative assembly annotation using DFAST

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.