## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29 ### :warning: Major enhancements - The Aspera CLI was recently added to [Bioconda](https://anaconda.org/bioconda/aspera-cli) 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](https://github.com/lukfor) for entertaining our requests and implementing them within upstream :heart:! ### Credits Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) - [Alexandru Mizeranschi](https://github.com/nicolae06) - [Alexander Blaessle](https://github.com/alexblaessle) - [Lukas Forer](https://github.com/lukfor) - [Matt Niederhuber](https://github.com/mniederhuber) - [Maxime Garcia](https://github.com/maxulysse) - [Sateesh Peri](https://github.com/sateeshperi) - [Sebastian Uhrig](https://github.com/suhrig) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes - [PR #238](https://github.com/nf-core/fetchngs/pull/238) - Resolved bug when prefetching large studies ([#236](https://github.com/nf-core/fetchngs/issues/236)) - [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Use wget instead of curl to download files from FTP ([#169](https://github.com/nf-core/fetchngs/issues/169), [#194](https://github.com/nf-core/fetchngs/issues/194)) - [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238) - [PR #245](https://github.com/nf-core/fetchngs/pull/246) - Refactor nf-test CI and test and other pre-release fixes ([#233](https://github.com/nf-core/fetchngs/issues/233)) - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3 - [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline. - [PR #253](https://github.com/nf-core/fetchngs/pull/253) - Add implicit tags in nf-test files for simpler testing strategy - [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12 - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253) - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68)) - [PR #261](https://github.com/nf-core/fetchngs/pull/261) - Revert sratools fasterqdump version ([#221](https://github.com/nf-core/fetchngs/issues/221)) - [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags - [PR #263](https://github.com/nf-core/fetchngs/pull/263) - Refine tags used for workflows - [PR #264](https://github.com/nf-core/fetchngs/pull/264) - Remove synapse workflow from pipeline - [PR #265](https://github.com/nf-core/fetchngs/pull/265) - Use "+" syntax for profiles to accumulate profiles in nf-test - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template - [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram - [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows - [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13 - [PR #288](https://github.com/nf-core/fetchngs/pull/288) - Update Github Action to run full-sized test for all 3 download methods - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline - [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map - [PR #295](https://github.com/nf-core/fetchngs/pull/295) - Be less stringent with test expectations for CI - [PR #296](https://github.com/nf-core/fetchngs/pull/296) - Remove params.outdir from tests where required and update snapshots - [PR #298](https://github.com/nf-core/fetchngs/pull/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.

## What's Changed * remove public_aws_ecr by @maxulysse in https://github.com/nf-core/fetchngs/pull/185 * Fix tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/187 * Adds emit statement for FASTQs and metadata to SRA workflow by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/184 * split up config files to be more modular by @maxulysse in https://github.com/nf-core/fetchngs/pull/186 * Move out multiQC and versions by @maxulysse in https://github.com/nf-core/fetchngs/pull/189 * tiny refactor by @maxulysse in https://github.com/nf-core/fetchngs/pull/190 * Update SRA workflow tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/191 * update tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/192 * FEAT: add changes by @maxulysse in https://github.com/nf-core/fetchngs/pull/193 * Recursively inherit configs by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/195 * remove all the nf-test logic from the refactor branch by @maxulysse in https://github.com/nf-core/fetchngs/pull/198 * restore nf-test tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/200 * forgot this file by @maxulysse in https://github.com/nf-core/fetchngs/pull/202 * fix path to file to include and update snapshots by @maxulysse in https://github.com/nf-core/fetchngs/pull/203 * Trying out initialise by @maxulysse in https://github.com/nf-core/fetchngs/pull/204 * Bump pipeline version to 1.11.0dev by @drpatelh in https://github.com/nf-core/fetchngs/pull/211 * nf-test POC by @maxulysse in https://github.com/nf-core/fetchngs/pull/201 * Per module/subworkflow tags.yml file by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/212 * Remove lib directory and replace with atomic subworkflows by @drpatelh in https://github.com/nf-core/fetchngs/pull/213 * update modules and tests + fix linting by @maxulysse in https://github.com/nf-core/fetchngs/pull/214 * FIX: custom/dumpsoftwareversions by @maxulysse in https://github.com/nf-core/fetchngs/pull/215 * add pipeline level tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/216 * Tag and path updates for nf-test files by @drpatelh in https://github.com/nf-core/fetchngs/pull/217 * Update workflows tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/218 * Update modules + tests by @maxulysse in https://github.com/nf-core/fetchngs/pull/219 * Use nf-core nfvalidation subworkflow by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/222 * Update nextflowpipelineutils by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/224 * Use nf-core subworkflow: NFCORE_PIPELINE_UTILS by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/223 * Fix all by @maxulysse in https://github.com/nf-core/fetchngs/pull/225 * fix sratools by @maxulysse in https://github.com/nf-core/fetchngs/pull/227 * Replace CUSTOM_DUMPSOFTWAREVERSIONS with collectFile operator by @adamrtalbot in https://github.com/nf-core/fetchngs/pull/226 * fix sratools and fewer ids by @maxulysse in https://github.com/nf-core/fetchngs/pull/228 * Prepare 1.11.0 RC by @maxulysse in https://github.com/nf-core/fetchngs/pull/230 * Refactor POC by @maxulysse in https://github.com/nf-core/fetchngs/pull/188 * Release candidate 1.11.0 by @maxulysse in https://github.com/nf-core/fetchngs/pull/231 **Full Changelog**: https://github.com/nf-core/fetchngs/compare/1.10.1...1.11.0

## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08 ### Credits Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) - [Harshil Patel](https://github.com/drpatelh) - [Maxime Garcia](https://github.com/maxulysse) - [Rob Syme](https://github.com/robsyme) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes - [#173](https://github.com/nf-core/fetchngs/issues/173) - Add compatibility for sralite files - [PR #205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile` - [PR #206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup - [PR #208](https://github.com/nf-core/fetchngs/pull/208) - Template update with nf-core/tools 2.10 ### Software dependencies | Dependency | Old version | New version | | ----------- | ----------- | ----------- | | `sra-tools` | 2.11.0 | 3.0.8 | > **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.

## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 ### Credits Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) - [Esha Joshi](https://github.com/ejseqera) - [Maxime Garcia](https://github.com/maxulysse) - [Moritz E. Beber](https://github.com/Midnighter) - [Rob Syme](https://github.com/robsyme) - [sirclockalot](https://github.com/sirclockalot) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes - [#85](https://github.com/nf-core/fetchngs/issues/85) - Not able to fetch metadata for ERR ids associated with ArrayExpress - [#104](https://github.com/nf-core/fetchngs/issues/104) - Add support back in for [GEO IDs](https://www.ncbi.nlm.nih.gov/geo) (removed in v1.7) - [#129](https://github.com/nf-core/fetchngs/issues/129) - Pipeline is working with SRA run ids but failing with corresponding Biosample ids - [#138](https://github.com/nf-core/fetchngs/issues/138) - Add support for downloading protected dbGAP data using a JWT file - [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data - [PR #140](https://github.com/nf-core/fetchngs/pull/140) - Bumped modules version to allow for sratools download of sralite format files - [PR #147](https://github.com/nf-core/fetchngs/pull/147) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8) - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower - [PR #157](https://github.com/nf-core/fetchngs/pull/157) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry ### Software dependencies | Dependency | Old version | New version | | --------------- | ----------- | ----------- | | `synapseclient` | 2.6.0 | 2.7.1 | > **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.