nf-core/fetchngs v1.12.0 - Titanium Platypus

[1.12.0] - 2024-02-29

⚠️ Major enhancements

• The Aspera CLI was recently added to Bioconda and we have added it as another way of downloading FastQ files in addition to the existing FTP and sra-tools support. In our limited benchmarks on all public Clouds we found ~50% speed-up in download times compared to FTP! FTP downloads will still be the default download method (i.e. --download_method ftp) but you can choose to use sra-tools or Aspera using --download_method sratools or --download_method aspera, respectively. We would love to have your feedback!
• The --force_sratools_download parameter has been deprecated in favour of using --download_method <method> to explicitly specify the download method; available options are ftp, sratools or aspera.
• Support for Synapse ids has been dropped in this release. We haven't had any feedback from users whether it is being used or not. Users can run earlier versions of the pipeline if required.
• We have significantly refactored and standardised the way we are using nf-test within this pipeline. This pipeline is now the current, best-practice implementation for nf-test usage on nf-core. We required a number of features to be added to nf-test and a huge shoutout to Lukas Forer for entertaining our requests and implementing them within upstream ❤️!

Credits

Special thanks to the following for their contributions to the release:

• Adam Talbot
• Alexandru Mizeranschi
• Alexander Blaessle
• Lukas Forer
• Matt Niederhuber
• Maxime Garcia
• Sateesh Peri
• Sebastian Uhrig

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

• PR #238 - Resolved bug when prefetching large studies (#236)
• PR #241 - Use wget instead of curl to download files from FTP (#169, #194)
• PR #242 - Template update for nf-core/tools v2.11
• PR #243 - Fixes for PR #238
• PR #245 - Refactor nf-test CI and test and other pre-release fixes (#233)
• PR #246 - Handle dark/light mode for logo in GitHub README properly
• PR #248 - Update pipeline level test data path to use mirror on s3
• PR #249 - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
• PR #253 - Add implicit tags in nf-test files for simpler testing strategy
• PR #257 - Template update for nf-core/tools v2.12
• PR #258 - Fixes for PR #253
• PR #259 - Add Aspera CLI download support to pipeline (#68)
• PR #261 - Revert sratools fasterqdump version (#221)
• PR #262 - Use nf-test version v0.8.4 and remove implicit tags
• PR #263 - Refine tags used for workflows
• PR #264 - Remove synapse workflow from pipeline
• PR #265 - Use "+" syntax for profiles to accumulate profiles in nf-test
• PR #266 - Make .gitignore match template
• PR #268 - Add mermaid diagram
• PR #273 - Update utility subworkflows
• PR #283 - Template update for nf-core/tools v2.13
• PR #288 - Update Github Action to run full-sized test for all 3 download methods
• PR #290 - Remove mentions of deprecated Synapse functionality in pipeline
• PR #294 - Replace mermaid diagram with subway map
• PR #295 - Be less stringent with test expectations for CI
• PR #296 - Remove params.outdir from tests where required and update snapshots
• PR #298 - export CONDA_PREFIX into container when using Singularity and Apptainer

Software dependencies

Dependency	Old version	New version
wget		1.20.1

NB: Dependency has been updated if both old and new version information is present.

NB: Dependency has been added if just the new version information is present.

NB: Dependency has been removed if new version information isn't present.

Parameters

Old parameter	New parameter
	--download_method
--input_type
--force_sratools_download
--synapse_config

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.