Skip to content

nf-core/fetchngs v1.7 - Sodium Skunk
Compare
Choose a tag to compare
@drpatelh drpatelh released this 01 Jul 16:12
· 786 commits to master since this release
1.7
b79cde2
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

[1.7] - 2022-07-01

⚠️ Major enhancements

Support for GEO ids has been dropped in this release due to breaking changes introduced in the NCBI API. For more detailed information please see this PR.

As a workaround, if you have a GEO accession you can directly download a text file containing the appropriate SRA ids to pass to the pipeline:

  • Search for your GEO accession on GEO
  • Click SRA Run Selector at the bottom of the GEO accession page
  • Select the desired samples in the SRA Run Selector and then download the Accession List

This downloads a text file called SRR_Acc_List.txt that can be directly provided to the pipeline e.g. --input SRR_Acc_List.txt.

Enhancements & fixes

  • #97 - Add support for generating nf-core/taxprofiler compatible samplesheets.
  • #99 - SRA_IDS_TO_RUNINFO fails due to bad request
  • Add enum field for --nf_core_pipeline to parameter schema so only accept supported pipelines are accepted
Assets 2
Loading