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Published August 27, 2021 | Version 2.0.0
Software Open

nf-core/bacass: v2.0.0 nf-core/bacass: "Navy Steel Swordfish"

Creators

  • 1. Boehringer Ingelheim
  • 2. QBiC
  • 3. @SciLifeLab | Karolinska Institutet
  • 4. NCCT
  • 5. Science for Life Laboratory
  • 6. Seqera Labs

Description

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

Files

nf-core/bacass-2.0.0.zip

Files (3.8 MB)

Name Size Download all
md5:f270978c8b2029c76acd5b6e2e5c0711
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Additional details

Related works

Is supplement to
https://github.com/nf-core/bacass/tree/2.0.0 (URL)