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v1.0 Espresso Myconaut

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@sateeshperi sateeshperi released this 25 Mar 16:07
· 252 commits to master since this release
v1.0
d977daf

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
Assets 2
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