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

Re-add support for addspecies #245

Merged
merged 8 commits into from
Mar 25, 2021
Merged

Re-add support for addspecies #245

merged 8 commits into from
Mar 25, 2021

Conversation

emnilsson
Copy link
Contributor

When I added the new way of accessing taxonomy-options, I did not think about the addspecies and realised I more or less just excluded it, especially from the test.config (I've re-added it there). But I'm not sure the way I handle it in ampliseq.nf is good - I did the same for ch_dada_ref_species as for ch_dada_ref_taxonomy but ch_dada_ref_species is never used. Maybe just change the --dada_ref_species to just evaluate if it's true or not?

@emnilsson emnilsson requested a review from d4straub March 24, 2021 12:42
@github-actions
Copy link

github-actions bot commented Mar 24, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8def2d6

+| ✅ 116 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   6 tests had warnings |!
### ❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
  • conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
  • conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

Run details

  • nf-core/tools version 1.13.2
  • Run at 2021-03-24 15:05:40

d4straub
d4straub reviewed Mar 24, 2021
View reviewed changes
conf/test.config Outdated
@@ -23,6 +23,7 @@ params {
input = "https://github.com/nf-core/test-datasets/raw/ampliseq/samplesheets/Samplesheet.tsv"
metadata = "https://github.com/nf-core/test-datasets/raw/ampliseq/samplesheets/Metadata.tsv"
dada_ref_taxonomy = "rdp=18"
dada_ref_species = "rdp=18"
Copy link
Collaborator

Choose a reason for hiding this comment

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

Since this is only a band-aid on a not required parameter I wait until you have removed it completely.

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Yes, working on it!

d4straub
d4straub approved these changes Mar 24, 2021
View reviewed changes
Copy link
Collaborator

@d4straub d4straub left a comment

Choose a reason for hiding this comment

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

Looks good!

@emnilsson emnilsson merged commit 805c25d into nf-core:DSL2 Mar 25, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@d4straub d4straub d4straub 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.
2 participants
@emnilsson @d4straub