phac-nml/fetchdatairidanext: Changelog

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

1.3.0 - 2024-02-19

`Added`

--provider parameter to be used to pick where to fetch data from and with what tool in PR #21.
- --provider SRA fetches data from the Sequence Read Archive
- --provider ENA fetches data from the European Nucleotide Archive

`Changed`

Updated nf-test snapshots and added new tests for --provider feature in PR #21.
Updated nextflow_schema.json with the --provider parameter in PR #21.
Updated dependency fasterq-dump to version 3.0.8 so that fasterq-dump can handle SRA Lite files in addition to SRA files in PR #23.

1.2.0

`Changed`

Modified the template for input csv file to include a sample_name column in addition to sample in-line with changes to IRIDA-Next update as seen with the speciesabundance pipeline
- If sample_name is supplied, then the reads will have sample_name prefixed before the accession code
- sample_name special characters will be replaced with "_"
Reverted fasterq-dump version to 2.11.0 from 3.0.8 due to issue #865. Solution proposed by fetchngs in PR #261
Fixed linting issues in CI caused by nf-core 3.0.1
Updated nf-test snapshots and added new tests for sample_name feature

1.1.1 - 2024-04-19

Added

Changed

Switched the resource label for prefetchchecker from process_low to process_single.
Switched GitHub continuous integration to test against at most Nextflow 23.10.1 (due to differences in outputs with later Nextflow pre-releases).

1.1.0 - 2024-04-10

Added

The ability to handle individual download errors. These errors will be reported in prefetch/failures_report.csv.

1.0.1 - 2024-02-22

Changed

Pinned nf-validation (@1.1.3) and nf-iridanext (@0.2.0) plugins to specific versions in nextflow.config

1.0.0 - 2024-01-26

Added

Initial release of fetchdatairidanext pipeline which will download reads from NCBI/INSDC archives.