1.5.2

What's Changed

• chore(deps): bump actions/checkout from 4 to 5 by @dependabot[bot] in #31
• Fix: fetch sra metadata retraction module by @gp201 in #32

Full Changelog: 1.5.0...1.5.2

1.5.0

What's Changed

• feat: Enhance version tracking by collecting software versions across workflows and processes by @gp201 in #27

Full Changelog: 1.4.1...1.5.0

1.4.1

What's Changed

• refactor: Update repository ownership in README and nextflow.config by @gp201 in #25
• fix: Update Nextflow version requirement to 24.10.0 in nextflow.config by @gp201 in #26

Full Changelog: 1.4.0...1.4.1

1.4.0

What's Changed

• feat: Add SRATOOLS_PREFETCH process and update workflows to include it; bump sra-tools version to 3.2.0 by @gp201 in https://github.com/gp201/flusra/pull/17
• Add docstrings for bin/fetch_sra_metadata.py by @gp201 in https://github.com/gp201/flusra/pull/18
• feat: Add hasNonZeroDepth function to filter out samples with no depth by @gp201 in https://github.com/gp201/flusra/pull/19
• feat: Update output handling in SRATOOLS_FASTERQDUMP to store .fastq.gz instead of .fastq; include pigz for compression by @gp201 in https://github.com/gp201/flusra/pull/22
• Add GENOFLU processes by @rrouz in https://github.com/gp201/flusra/pull/21
• feat: Add Dependabot configuration for monthly updates of GitHub Actions by @gp201 in https://github.com/gp201/flusra/pull/23
• refactor: Remove sorting of merged results in merge_genoflu_results function by @gp201 in https://github.com/gp201/flusra/pull/24

New Contributors

• @rrouz made their first contribution in https://github.com/gp201/flusra/pull/21

Full Changelog: gp201/flusra@1.3.1...1.4.0

1.3.1

What's Changed

• feat: add demix_lineage_hierarchy parameter to FREYJA_DEMIX process and update Milk_Freyja workflow by @gp201 in https://github.com/gp201/flusra/pull/13
• fix: update XML parsing logic in fetch_sra_metadata to correctly retrieve LibraryLayout and Platform fields by @gp201 in https://github.com/gp201/flusra/pull/16
• feat: Add support for single-ends reads by @gp201 in https://github.com/gp201/flusra/pull/14

Full Changelog: gp201/flusra@1.2.1...1.3.1

1.2.1

What's Changed

• fix: add trimming configuration parameter to FETCH_SRA_METADATA function by @gp201 in https://github.com/gp201/flusra/pull/5
• fix: update condition to use samples_to_process in workflow by @gp201 in https://github.com/gp201/flusra/pull/6
• Hot fix fetch sra metadata by @gp201 in https://github.com/gp201/flusra/pull/7
• fix: change output file extension from .csv to .tsv in FETCH_SRA_METADATA process by @gp201 in https://github.com/gp201/flusra/pull/8
• fix: update FETCH_SRA_METADATA output to split TSV instead of CSV by @gp201 in https://github.com/gp201/flusra/pull/9
• fix: Update Freyja modules for version extraction and add conditional logic to Milk_Freyja sub-workflow by @gp201 in https://github.com/gp201/flusra/pull/10
• feat: Add feature to track retracted runs by @gp201 in https://github.com/gp201/flusra/pull/11
• feat: update freyja dependency version to 1.5.3 in environment files to use autoadapt feature by @gp201 in https://github.com/gp201/flusra/pull/12

Full Changelog: gp201/flusra@1.1.0...1.2.1

1.1.0

What's Changed

• Update process handling by @gp201 in https://github.com/gp201/flusra/pull/3
• Introduce FASTP module for trimming by @gp201 in https://github.com/gp201/flusra/pull/4

Full Changelog: gp201/flusra@1.0.0...1.1.0

1.0.0

Merge pull request #2 from gp201/gff_support

Add support for using gff files