Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add support for dbGAP data with JWT #152

Merged
merged 21 commits into from
May 15, 2023
Merged

Add support for dbGAP data with JWT #152

merged 21 commits into from
May 15, 2023

Conversation

ejseqera
Copy link
Contributor

@ejseqera ejseqera commented May 9, 2023 •
edited
Loading

Addresses #138 by adding support for optional JWT file to be used in prefetch and fasterqdump to download protected dbGAP runs.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/fetchngs branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@ejseqera ejseqera added the enhancement Improvement for existing functionality label May 9, 2023
@ejseqera ejseqera added this to the 1.10.0 milestone May 9, 2023
@ejseqera ejseqera self-assigned this May 9, 2023
@github-actions
Copy link

github-actions bot commented May 9, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b0d32c2

+| ✅ 149 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: '1.10.0'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: dbgap_key

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-15 19:35:38

@ejseqera ejseqera mentioned this pull request May 9, 2023
Closed
@ejseqera ejseqera requested a review from drpatelh May 9, 2023 05:06
drpatelh
drpatelh reviewed May 13, 2023
View reviewed changes
nextflow_schema.json Outdated Show resolved Hide resolved
drpatelh
drpatelh reviewed May 14, 2023
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
drpatelh
drpatelh reviewed May 14, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
drpatelh
drpatelh reviewed May 14, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
@drpatelh drpatelh mentioned this pull request May 14, 2023
Merged
drpatelh
drpatelh reviewed May 15, 2023
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
@ejseqera ejseqera requested a review from drpatelh May 15, 2023 17:07
drpatelh
drpatelh reviewed May 15, 2023
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
drpatelh
drpatelh reviewed May 15, 2023
View reviewed changes
workflows/sra.nf Outdated Show resolved Hide resolved
@ejseqera ejseqera requested a review from drpatelh May 15, 2023 19:34
@drpatelh drpatelh merged commit 1dbc8bf into nf-core:dev May 15, 2023
4 of 10 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@drpatelh drpatelh Awaiting requested review from drpatelh

Assignees

@ejseqera ejseqera

Labels
enhancement Improvement for existing functionality
Projects
None yet
Milestone
1.10.0
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@ejseqera @drpatelh