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

update with zipped indices #662

Merged
merged 9 commits into from
Jul 21, 2022
Merged

update with zipped indices #662

merged 9 commits into from
Jul 21, 2022

Conversation

FriederikeHanssen
Copy link
Contributor

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

@github-actions
Copy link

github-actions bot commented Jul 19, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f87517f

+| ✅ 144 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.0'
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-21 09:36:17

SusiJo
SusiJo approved these changes Jul 20, 2022
View reviewed changes
Copy link
Contributor

@SusiJo SusiJo left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Nice! 🚀

asp8200
asp8200 reviewed Jul 20, 2022
View reviewed changes
conf/igenomes.config Outdated Show resolved Hide resolved
@asp8200
Copy link
Contributor

asp8200 commented Jul 20, 2022

I just tried to see if I could download the newly referenced file af-only-gnomad.hg38.vcf.gz, but it didn't work out:

$ aws s3 --no-sign-request cp s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz .
fatal error: An error occurred (404) when calling the HeadObject operation: Key "igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz" does not exist

By doing the following command, I was able to download the GATKBundle, but it didn't include af-only-gnomad.hg38.vcf.gz :

aws s3 --no-sign-request cp s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle . --recursive

What am I doing wrong? Isn't the file af-only-gnomad.hg38.vcf.gz included in the GATKBundle yet?

@FriederikeHanssen
Copy link
Contributor Author

the files didn't actually copy over apparently. I wish the aws cli would then actually fail and report that no files were moved.

maxulysse
maxulysse approved these changes Jul 20, 2022
View reviewed changes
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

OK to merge when files are actually there

@maxulysse
Copy link
Member

Actually, can you update the usage.md with these updated files?

@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 20, 2022
Merged
11 tasks
@maxulysse
Copy link
Member

Can we add the new known_snps to https://github.com/nf-core/sarek/blob/dev/docs/usage.md#where-do-the-used-reference-genomes-originate-from

@apeltzer apeltzer added this to the 3.0 milestone Jul 21, 2022
@maxulysse maxulysse merged commit 2290c7f into nf-core:dev Jul 21, 2022
@FriederikeHanssen FriederikeHanssen deleted the update_igenomes branch July 10, 2023 19:01
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@asp8200 asp8200 asp8200 left review comments

@SusiJo SusiJo SusiJo approved these changes

@apeltzer apeltzer apeltzer approved these changes

@maxulysse maxulysse maxulysse approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
3.0
Development

Successfully merging this pull request may close these issues.
5 participants
@FriederikeHanssen @asp8200 @maxulysse @apeltzer @SusiJo