Release v1.1.3

Small patch to fix the workflow crashing on bcftools sort when running as a standalone job within large clusters

v1.1.2

Minor fix preventing the workflow to start when launched from the repository directly.

Release v1.1.0

Release v1.1.0 adds a smörgåsbord of changes, listed in the changelog below.

Added

• Create a "smile plot" for the derived allele frequencies (DAF)
• Demo data to test the workflow; in the future, the workflow will have CI testing to ensure basic features' stability
• Add a filtering step removing variants with derived allele frequency above a given threshold (default 0.98)

Changed

• Docker dependencies
• DAF are computed in preprocessing, and saved as output file
• Introduced three separate options to trigger the different components: --relate, --mutyper and --sdm (runs mutyper only as default)
• --relate_path is now used to provide the path to the relate installation directory instead of --relate
• --ancestral is now --ancestral_fna, and --ref_fasta is now --fasta_fna
• Faster preprocessing of the VCF by processing by contig wherever possible
• Faster VCF I/O thanks to dropping most INFO fields when extracting biallelic sites
• Separate the filtered SDM sites based on whether they fall into a repeat masked region or not
• Increased threads provided to selected bcftools processes
• Ancestral genome now uses cactus official image, rather than on the downloaded tools
• The workflow now uses chunking whereever possible to speed up processing, defined by chunk_size
  • The chunk size can be slightly higher when consecutive sites are found, effectively splitting only when breaks in variants are identified
  • Both Mutyper and SDM subworkflows takes advantage of the approach, reducing redundancy of the analyses and allowing lower I/O with faster analysis of data
• Collection of mutation type is now performed by sequence, rather on the full dataset
• Greatly increase performances of bed2vbed process by heavy usage of polars dataframes, an improved logic and decreased I/O operations (see table):

Version	Mode	Memory (GB)	Runtime (min)	Fold improv.
v1.0.0	-	0.7	18.9	1.0x
v1.1.0	Memory	11.3	5.9	3.2x
v1.1.0	Greedy	25.0	4.0	4.7x

Fixed

• Fixes a start-up issue when running from the directory, rather than from main.nf
• Fixes -stub runtime issues
• Mutyper plots ignoring groupings

Removed

• Legacy DSL1 code (legacy/main.nf)
• Dropped filtering process as unused in the analyses
• BED2VBED and COMBINE scripts

Release 1.0.0

v1.0.0

Fix suffix naming in output from custom counting of mutation spectrum