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

tweak usage.md #68

Merged
merged 5 commits into from
Oct 13, 2023
Merged

tweak usage.md #68

merged 5 commits into from
Oct 13, 2023

Conversation

allaway
Copy link
Contributor

@allaway allaway commented Oct 13, 2023

To (partially?) address #67, minor adjustment to docs. 😄

I believe these are the only two relevant checkboxes for this PR:

  • This comment contains a description of changes (with reason).
  • Usage Documentation in docs/usage.md is updated.

@allaway
tweak usage.md
6ef61ef 
To (partially?) address nf-core#63.
@FriederikeHanssen
Copy link
Contributor

Hey! Thanks for fixing the docs. In fact, looks like the file_type is also mandatory :

bamtofastq/assets/schema_input.json

Line 37 in c70f49b

"required": ["sample_id", "mapped", "file_type"]
. Could you add that?

@allaway
Copy link
Contributor Author

allaway commented Oct 13, 2023

Hey! Thanks for fixing the docs. In fact, looks like the file_type is also mandatory :

bamtofastq/assets/schema_input.json

Line 37 in c70f49b

"required": ["sample_id", "mapped", "file_type"]

. Could you add that?

Ah, ok, that makes sense as to why the docs originally said three columns are required. I'll fix this!

@allaway
Copy link
Contributor Author

allaway commented Oct 13, 2023

@FriederikeHanssen - let me know if you would like to see any other changes! I also made some changes to make the column names more consistent in the docs.

@github-actions
Copy link

github-actions bot commented Oct 13, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9bf7b9a

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.0
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in WorkflowBamtofastq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-13 21:27:29

@FriederikeHanssen
Copy link
Contributor

@nf-core-bot fix linting

FriederikeHanssen
FriederikeHanssen approved these changes Oct 13, 2023
View reviewed changes
Copy link
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

Wonderful, thanks a lot 😊 just waiting for the bot to fix linting and then can merge

@FriederikeHanssen FriederikeHanssen merged commit b4c15ee into nf-core:dev Oct 13, 2023
20 checks passed
@asp8200 asp8200 mentioned this pull request Feb 20, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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

Successfully merging this pull request may close these issues.
3 participants
@allaway @FriederikeHanssen @nf-core-bot