[1.12.0] - 2024-02-29 :warning: 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 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 :heart:! 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.