v2.1.0 nf-core/bacass: "Navy Steel Swordfish" - 2023/10/20

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

• #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