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nf-core/mycosnp: Changelog

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

v1.3 Musky Albus - [06/09/2022]

Added

Fixed

  • Changed downsample strategy in modules/local/downsample_rate.nf that was causing differences with results from geneflow version. Downsample rate now set at default 1 (closes #67)

Dependencies

Deprecated

TODO

v1.2 Expecto Patronum - [05/11/2022]

Added

  • Changed minimum time requirements in base.config for process_low, process_medium, process_high to 72.h and process_long to 120.h.
  • SNP distance matrix addition as output.
  • Updated qc_report.txt to include coverage mean depth and reads mapped.
  • Positions masked (N) based on DP & Added functionality to use min_depth (Default 50).
  • Change test profile to include min_depth = 2 so it will run to completion.

Fixed

  • Bug fix for downsample mismatch.
  • Change configuration variable name from vcftools_filter to gatkgenotypes_filter.
  • Changed samplesheet creation to accept multiple directories as arguments and to recursively search for sequences.
  • Set full vcf consensus file to debug output
  • Remove part nf-core branding

Dependencies

Deprecated

TODO

  • Update logo

v1.1 Candid Aura - [04/01/2022]

Added

Fixed

  • Fixed bug in modules/local/lane_merge.nf that was causing samplesheet CSV file to not recognize R2 (closes #39)
  • Formatting of docs/output.md
  • Changed output file combined/vcf-to-fasta/combined_vcf-to-fasta.fasta -> combined/vcf-to-fasta/vcf-to-fasta.fasta
  • Output file combined/vcf-to-fasta/vcf-to-fasta.fasta will now replace stars * with dashes -
  • Output file combined/phylogeny/rapidnj/rapidnj_phylogeny.tre -> combined/phylogeny/rapidnj/rapidnj_phylogeny.nh
  • Output file combined/phylogeny/iqtree/vcf-to-fasta.fasta.treefile -> combined/phylogeny/iqtree/iqtree_phylogeny.nh
  • Output file combined/phylogeny/raxmlng/output.raxml.bestTree -> combined/phylogeny/raxmlng/raxmlng_bestTree.nh
  • Output file combined/phylogeny/raxmlng/output.raxml.support -> combined/phylogeny/raxmlng/raxmlng_support.nh

Dependencies

Deprecated

  • /results/qc output dir removed

TODO

  • Continue improving output docs

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