v1.3.0

1.3.0 (2023-10-07)

Features

• add a mock test dataset for faster test run (8609a09)
• add an option to rename duplicates before seqkit sort (bfefd72)
• update main config.yaml (d63291e)

Bug Fixes

• fixed the issues with na p-values (c577d86)
• make igv_report optional so the pipeline can run without providing a gff/gtf file (61105b8)

v1.2.4

1.2.4 (2023-09-19)

Features

• add user defined manhattan plot parameters (b71f0fb)

Bug Fixes

• fixed qmplot link for the report (0dec539)
• fixed typo in rule bowtie2_build (#19) (9ef6faf)

Performance Improvements

• changed snakemake to snakemake-minimal (8f85998)

v1.2.3

1.2.3 (2023-05-09)

Features

• added init func. to initialize a new workdir (be02e7f)
  • kgwasflow init initializes a new kGWASflow working directory with the default configuration and test files.

Bug Fixes

• fixes broken input path (bcc1606)

v1.2.2

1.2.2 (2023-05-03)

Bug Fixes

• fixed the issue with missing package data (4573f50)

v1.2.1

1.2.1 (2023-04-24)

Features

• add python cli support (56ca35c)
• add setup and manifest (d15224a)

v1.2.0

1.2.0 (2023-04-17)

Features

• add a function to extract chromosome names and lengths from a SAM file (413ead9)
• add a rule for genome indexing (f2d596e)
• add a rule to convert BAM files to BED (a948d98)
• add a rule to convert kmers table to PLINK (8c4bfad)
• add error handling (da92bdb)
• add k-mer counts dist. plots (7df4787)
• add k-mer counts dist. plots (79427b4)
• add k-mer counts dist. plots (c45c412)
• add kGWASflow.py (698dcb8)
• add new functions, update checkpoints + target outputs (6dac404)
• add rules for converting BAM to BED (33ed058)
• add rules for generating igv reports (igv-report) (2c4b4fe)
• improve the kmers GWAS summary reports (9d5de9e)

Bug Fixes

• change output, log paths and report caption (827dcad)
• make the script compatible with new kmers GWAS summary reports (3dbecf0)
• specify the spades version (35d5690)
• update input file paths (05d7e6b)
• update input, output and params paths (4637ed6)
• update output directory paths + add touch (a0500c2)

Performance Improvements

• update snakemake version to 7.25.0 (5b999c4)
• update to fasterq-dump wrapper v1.23.5 (373b406)
• update blast wrapper to v1.25.0 (3da03ba)
• update to kmc 3.2.1 (c933fda)

v1.1.0

Features:

• update to latest kmersGWAS version v.0.3 (84cfb9f)
• update min snakemake version to 7.18.2

Full Changelog: v1.0.0...v.1.1.0

v1.0.0

Initial stable release of kGWASflow.

Full Changelog: v0.1.0-beta...v1.0.0

Version 0.1.0-beta (Pre-release)

Initial pre-release

Full Changelog: https://github.com/akcorut/kGWASflow/commits/v0.1.0-beta