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