v2.3.1 nf-core/bacass: “Navy Iron Oyster” 2024/06/24

Changed

Added

Fixed

• #147 Fixed input file errors related to samplesheets containing relative paths to symbolic links, addressing the ‘not a valid path’ error.

Dependencies

Deprecated

v2.3.0 nf-core/bacass: “Navy Iron Oyster” 2024/06/12

Changed

• #135 Replaced nf-core MultiQC module with a custom MultiQC module.

Added

• #135 Implementation of KmerFinder subworkflow Custom Quast, and Custom MultiQC Reports:

  • Added KmerFinder subworkflow for read quality control, purity assessment, and sample grouping based on reference genome estimation.
  • Enhanced Quast Assembly QC to run both general and reference genome-based analyses when KmerFinder is invoked.
  • Implemented custom MultiQC module with multiqc_config.yml files for different assembly modes (short, long, hybrid).
  • Generated custom MultiQC HTML report consolidating metrics from KmerFinder, Quast, and other relevant sources.

• #133 Update nf-core/bacass to the new nf-core 2.14.1 TEMPLATE.

Fixed

• #134 - Fixed samples reported of prokka/bakta in multiqc report.

• #125 - Fixed conflicting settings in save_trimmed_fail parameter.

Dependencies

Deprecated

v2.2.0 nf-core/bacass: “Aqua Platinum Zebrafish” 2024/03/27

Changed

• #111 - Update nf-core/bacass to 2.12, and #117 to 2.13.1 TEMPLATE.

Added

• #104, #106 - Added dragonflye module and enbled draft genome polishing with short-reads.

Fixed

• #123 - Add fallback to download_pipeline.yml when the pipeline does not support stub runs (#2846)

Dependencies

• #120 - Update local and nf-core modules (version update an minnor code changes).

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

• #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.

• Update already nf-core modules

• Refactor local/modules making them follow nf-core v2.9 structure/fashion.

Deprecated

• #86 Replace depecated modules with nf-core/modules.

  • Replace local/get_software_versions.nf with nf-core/custom/dumpsoftwareversions.nf
  • Replace 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

• #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.