v1.5 Wingardium Leviosa - [05/09/2023]

Re-released on 09/03/2024 following #122 (disabled snpEff logging - no changes in functionality)

Added

• Added new subworkflow for snpEff variant annotation
• Added Quicksnp module which creates a neighbor-joining tree with SNP distances on branches

Fixed

• Corrected an issue with downsampling read count calculations

Dependencies

• N/A

Deprecated

• Removed rate parameter to use coverage instead

TODO

• Update file naming for snpEff mutations file

v1.4 Tremella Snidget - [06/27/2022]

Added

• Added containers for processes which did not have any container specified.

Fixed

• Changed default --min-depth to 10

Dependencies

Deprecated

TODO

---

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

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

---

Issues closed:

• Reference genome inherited at positions with zero read support #45
• Read count for the same sample varies in the qc_report #47
• update configuration file for vcftools_filter clarity #51
• Updating QC_REPORT with mean depth and % mapped reads #53
• #58

What's Changed

• Remove extra tabs in qc_report and replace += on list by @rpetit3 in #46
• bug fix for downsample mismatch by @mciprianoCDC in #54
• Dev qcfiltervar by @mciprianoCDC in #55
• Dev mycosnp samplesheet by @mciprianoCDC in #57
• mask positions based on DP by @rpetit3 in #59
• Dev usedp by @mciprianoCDC in #62
• Dev optionsdebug by @mciprianoCDC in #64
• Changed time requirements in base.config by @jforstedt in #65
• Issue #53: Updating QC report by @cjjossart in #61
• v1.2 by @sateeshperi in #66

New Contributors

• @jforstedt made their first contribution in #65

Full Changelog: v1.1...v1.2

v1.1

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

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