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Recent Releases of mycosnp-nf

mycosnp-nf - v1.6.3 - [07/25/2025]

Fixed

  • [Pre-MycoSNP workflow] GC content calculation for closest GAMBIT match (Reference_GC field in pre-mycosnp-summary.csv) excluded lowercase (soft-masked) bases, i.e. "c" and "g", leading to underestimates for Reference_GC. This fix includes lowercase "g" and "c" in the GC content calculation in bin/pre-mycosnp-stats.sh, for both the closest GAMBIT match and the sample assembly. However, the sample assembly shouldn't contain any soft-masked bases to begin with, so this shouldn't result in any differences in Sample_Assembly_GC.

- Nextflow
Published by zmudge3 11 months ago

mycosnp-nf - v1.6.2 - [05/18/2025]

Fixed

  • Docker permissions issue with GAMBIT container in some Linux environments (issue #137)

Changed

  • Bumped GAMBIT fungal database from v0.2.0 to v1.0.0. See GAMBIT'S documentation for details about the databases.
  • Bumped GAMBIT version from v1.0.0 to v1.1.0. Database is now included with the repo in assets/gambit_db/. Signatures database in assets/gambit_db/signatures/ (split into chunks so each chunk is below GitHub's file size limit of 100 MB and warning limit of 50 MB). See GAMBIT v1.1.0 release notes for more info (no functional changes).

- Nextflow
Published by zmudge3 about 1 year ago

mycosnp-nf - v1.6.1 - [05/09/2025]

Changed

  • Switched Shovill container image to StaPH-B's Docker image (quay.io/staphb/shovill:1.1.0-2022Dec). Addresses issues with pulling image from Docker Hub (#134).
  • Reordered params in nextflow_schema.json to be more intuitive.

- Nextflow
Published by zmudge3 about 1 year ago

mycosnp-nf - v1.6.0 - [04/21/2025]

Added

  • Added the "Pre-MycoSNP" workflow for quick fungal taxonomic classification and Candida auris clade typing (using de novo assemblies)
    • Base workflow development by Jared Johnson @DOH-JDJ0303 (#119)
    • Original sourmash subtyping subworkflow by Charlotte Royer @royercj (#114)
    • Co-development, validation, testing, and documentation by Zack Mudge @zmudge3
  • Added the "Genome Fraction" metric to the main MycoSNP workflow's QC report, by CJ Jossart @cjjossart (#123, #128)
  • Nextflow Tower / Seqera Cloud functionality, by Jared Johnson @DOH-JDJ0303 (#104)
  • Added FKS1 coordinates for a third hotspot region (single amino acid) associated with echinocandin resistance in Candida auris (for the snpeffr report - results/snpeff/combined_cauris_refB11205_fks1.csv)

Changed

  • Bumped GATK version to 4.5.0.0
  • Changed SnpEff-related config to work with cloud, by Jared Johnson @DOH-JDJ0303 (#103)
  • Updated samplesheet and reference genome links in test.config
  • Changed filename of results/snpeff/combined.csv to results/snpeff/combined_cauris_refB11205_fks1.csv
  • Bumped snpeffr version to v1.1.1. The "mutation" column in the snpeffr report (results/snpeff/combined_cauris_refB11205_fks1.csv) can now contain a value of "undetermined". This occurs when GATK identifies a variant in the individual VCF file for an isolate, but then the identified variant is lost in the subsequent step when GATK creates a merged VCF file that includes all isolates.

Removed

Fixed

  • Fixed Candida auris FKS1 hotspot 1 coordinates in nextflow.config, to include the first nucleotide of F635, and remove two extra nucleotides at the end

Deprecated

  • Nextflow -entry parameter to run specific workflow is deprecated. Use MycoSNP's --workflow parameter instead.

- Nextflow
Published by zmudge3 about 1 year ago

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

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

- Nextflow
Published by hseabolt about 3 years ago

mycosnp-nf - 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


- Nextflow
Published by mciprianoCDC almost 4 years ago

mycosnp-nf - ## 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


- Nextflow
Published by mciprianoCDC about 4 years ago

mycosnp-nf - 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 vcftoolsfilter to `gatkgenotypesfilter`.

  • 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 qcreport #47 * update configuration file for vcftoolsfilter clarity #51 * Updating QC_REPORT with mean depth and % mapped reads #53 * https://github.com/CDCgov/mycosnp-nf/issues/58

What's Changed

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

New Contributors

  • @jforstedt made their first contribution in https://github.com/CDCgov/mycosnp-nf/pull/65

Full Changelog: https://github.com/CDCgov/mycosnp-nf/compare/v1.1...v1.2

- Nextflow
Published by sateeshperi about 4 years ago

mycosnp-nf - 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

- Nextflow
Published by sateeshperi about 4 years ago

mycosnp-nf - 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

- Nextflow
Published by sateeshperi about 4 years ago