v1.0 Espresso Myconaut

nf-core/mycosnp: Changelog

The format is based on Keep a Changelog
and this project adheres to Semantic Versioning.

v1.0 Espresso Myconaut - [03/25/2022]

Initial release of CDCgov/mycosnp-nf, created with the nf-core template.

Added

• Added test and test_full profiles for easy testing
• Support for phylogenetic tree generation --rapidnj --fasttree --iqtree --raxmlng
• Skip reference generation --ref_dir | assets/precomputed/reference available for testing
• Add SRA ids to download from NCBI --add_sra_file | assets/sra_small.csv assets/sra_large.csv available for testing
• Add vcf files generated from previous runs --add_vcf_file | assets/precomputed/vcf available for testing
• Skip combined variant analysis (run reference prep and mapping) skip_combined_analysis
• Skip samples capability --skip_samples
• Skip samples file capability --skip_samples_file

Fixed

Dependencies

• Nextflow
• nf-core

Deprecated

• GeneFlow support
• QC pdf report

TODO

• Intermediate file cleanup and management
• Update logo and metro-style workflow