v1.1.0 - Polite Platyfish

Enhancements & fixes

• Upgrade to the version 2.8 of the nf-core template.
• nf-core module updates to remove Anaconda references
• Updated configuration of the GitHub CI to improve testing.
• Simpler samplesheet format, with just the path to the Fasta file and the output directory.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
htslib		1.20
MultiQC	1.13	1.20
Python	3.8.3,3.9	3.9.1
samtools		1.21

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

v1.0.0 – Apophis

Overview

The pipeline takes an assembly Fasta file (possibly compressed), runs fasta_windows on it, and transforms the outputs into files more practical for downstream use.

Steps involved:

• Run fasta_windows on the assembly Fasta file.
• Extract single-statistics bedGraph files from the multi-statistics TSV
  files fasta_windows outputs.
• Compress and index all bedGraph and TSV files with bgzip and tabix.

Dependencies

All dependencies are automatically fetched by Singularity.

• fasta_windows
• bgzip
• tabix
• python3
• awk
• gzip