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phac-nml/mikrokondo: Changelog

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

0.5.0 - 2024-11-27

Added

  • Added RASUSA for down sampling of Nanopore or PacBio data. PR 125

  • Added a new sample_name field to the schema_input.json file: PR 140

  • Incorporated a --skip_read_merging parameter to prevent read merging PR 140

Changed

  • Added a sample_name field, sample still exists but is used to incorporate additional names/identifiers in IRIDANext PR 140

  • RASUSA now used for down sampling of Nanopore or PacBio data. PR 125

  • Default Listeria quality control parameters apply only to monocytogenes now. PR 142

Updated

  • Documentation and workflow diagram has been updated. PR 123

  • Documentation and Readme has been updated. PR 126

  • Adjusted schema_input.json to allow for non-gzipped inputs. PR 137

  • Updated github actions workflows for nf-core version 3.0.1. PR 137

0.4.2 - 2024-09-25

Fixed

  • Fixed broken link in readme. PR 117

  • Fixed ectyper parameter types in the nextflow_schema.json from number to integer. PR 121

0.4.1 - 2024-09-16

Fixed

  • Fixed null species ID in QCMessage when no organism qc data available. PR 111

Changed

  • Removed missing alleles from final report fixing issue 112.

  • Changed default option for override_allele_scheme from null to "" (evaluates to false). PR 109

0.4.0 - 2024-09-04

Changed

  • Removed quay.io docker repo tags PR 94

Updated

  • Added QCMessage and QCSummary fields for metagenomic sequencing runs. See PR 103

  • Updated TSeemann's MLST default container to use version 2.23.0 of mlst. See PR 97

  • Moved allele schema parameters under one option in the nextflow_schema.json. See PR 104

Fixed

  • Fixed typo in metagenomic QC message. See PR 103

  • Fixed spelling issues issues in config values. See PR 95

  • Fixed the headers specified in the nextflow.config file for Kraken2. See PR 96

Added

  • Added additional organism QC parameters to defaults. See PR 105

  • Updated locidex to version 0.2.3. See PR 96

  • Added module for automatic selection of locidex databases through configuration of a locidex database collection. See PR 96

  • Added module for summary of basic allele metrics, listing of missing alleles and reporting of specific alleles. See PR 96

0.3.0 - 2024-07-04

Changed

  • Reformatted QCSummary fields and added a QCMessage field containing the old summary message. See PR 85

  • Changed default Python3 image to use the StarAMR image. See PR 90

  • Stripped identifier from taxonomic identification from string. See PR 90

  • Removed retry logic from processes and switched them to ignore. See PR 91

Fixed

  • Updated samtools/minimap2 container fixing CI issues and issues running the pipeline with Docker. See PR 85

  • Removed task.maxRetries from error handling to prevent StackOverflow addressing PR 91

Added

  • Altered name of stored SpeciesTopHit field in the irida-next.config, and added a field displaying the field name used addressing PR 90

0.2.1 - 2024-06-03

Fixed

  • Parsed table values would not show up properly if values were missing resolving issue See PR 83
  • Fixed mismatched description for minimap2 and mash databases. See PR 83

0.2.0 - 2024-05-14

Added

  • Updated documentation for params. See PR 66

  • Fixed param typos in schema, config and docs. See PR 66

  • Added parameter to skip length filtering of sequences. See PR 66

  • Added locidex for allele calling. See PR 62

  • Updated directory output structure and names. See PR 66

  • Added tests for Kraken2 contig binning. See PR 66

Fixed

  • If you select to filter contigs by length, those contigs will now be used for subsequent analysis. See PR 66

  • Matched ECTyper and SISTR parameters to what is set in the current IRIDA. See PR 68

  • Updated StarAMR point finder DB selection to resolve error when in db selection when a database is not selected addressing issue. See PR 74

  • Fixed calculation of SeqtkBaseCount value include counts for both pairs of paired-end reads. See PR 65.

Changed

  • Changed the specific files and metadata to store within IRIDA Next. See PR 65

  • Added separate report fields for (PASSED|FAILED|WARNING) values and for the the actual value. See PR 65

  • Updated StarAMR to version 0.10.0. See PR 74

0.1.2 - 2024-05-02

Changed

  • Changed default values for database parameters --dehosting_idx, --mash_sketch, --kraken2_db, and --bakta_db to null. See PR 71
  • Enabled checking for existence of database files in JSON Schema to avoid issues with staging non-existent files in Azure. See PR 71.
  • Set --kraken2_db to be a required parameter for the pipeline. See PR 71
  • Hide bakta parameters from IRIDA Next UI. See PR 71

0.1.1 - 2024-04-22

Changed

  • Switched the resource labels for parse_fastp, select_pointfinder, report, and parse_kat from process_low to process_single as they are all configured to run on the local Nextflow machine. See PR 67

0.1.0 - 2024-03-22

Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trimming and quality control, contamination detection, assembly (isolate, metagenomic or hybrid), annotation, AMR detection and subtyping of genomic sequencing data targeting bacterial or metagenomic data.

  • Bumped version number to 0.1.0

  • Updated docs to include awesome-page plugin and restructured readme.

  • Updated coverage defaults for Shigella, Escherichia and Vibrio

  • Updated file outputs to match the nf-iridanext plug-in

  • Incorporated IRIDANext plug-in

  • Upgraded nf-validation to latest version 2.0.0

  • Added message to final summary report notifying user if an assembly does not have any contigs exceeding the minimum contig length parameter

  • Added contig count check before running Quast to ensure empty files are not passed in.

  • Added process to filter contigs based on a minimum required contig length.

  • Added option to force sample to be implemented as an isolate

  • Changed salmonella default default coverage to 40

  • Added integration testing using nf-test.