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

Zip prodigal outputs (closes #922) #3136

Merged
merged 10 commits into from
Mar 28, 2023
Merged

Zip prodigal outputs (closes #922) #3136

merged 10 commits into from
Mar 28, 2023

Conversation

kedhammar
Copy link
Contributor

PR checklist

Closes #922

Use pigz to gzip all prodigal output files.

@kedhammar kedhammar added enhancement New feature or request good first issue Good for newcomers update module Ready for Review hackathon2023 Topic for the hackathon of March 2023 labels Mar 27, 2023
SPPearce
SPPearce reviewed Mar 28, 2023
View reviewed changes
Copy link
Contributor

@SPPearce SPPearce left a comment

Choose a reason for hiding this comment

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

You will need to update the tests to correspond to the files changed.
Are you aiming for zip or gz? As you have .zip in the file paths but no longer -K in the command.

@kedhammar
Copy link
Contributor Author

Thanks @ SPPearce!

I've update the command as well as the expected test results.

@kedhammar kedhammar requested a review from SPPearce March 28, 2023 09:25
@kedhammar kedhammar added this pull request to the merge queue Mar 28, 2023
Merged via the queue into nf-core:master with commit 8c4f2d2 Mar 28, 2023
jvfe added a commit to jvfe/modules that referenced this pull request Mar 28, 2023
@jvfe
Merge branch 'master' into islandpath
09cb357 
* master:
  Rename spatialomics to imaging in test_data.config (nf-core#3164)
  Freyja subworkflow with required modules (nf-core#3003)
  Version update for sourmash modules (nf-core#3159)
  update UMI subworkflow with duplex and best practices (nf-core#3104)
  Zip prodigal outputs (closes nf-core#922) (nf-core#3136)
  new module: pyrodigal (nf-core#3165)
  Group all mus_musculus together (nf-core#3170)
  PEDDY: added prefix to the name of outputs (nf-core#2984)
  Fix WFMASH error - missing variable (nf-core#3155)
  Updating endorspy (nf-core#3134)
  Limma: mandatory non-file args update, add subset options for differential analysis (nf-core#3116)
  sambamba flagstat module (nf-core#3133)
  Wisecondorx/convert (nf-core#3131)
  Metaphlan/makedb (nf-core#3138)
  New module Ilastik/multicut (nf-core#2894)
@louperelo louperelo mentioned this pull request May 10, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@SPPearce SPPearce SPPearce approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

Assignees
No one assigned
Labels
enhancement New feature or request good first issue Good for newcomers hackathon2023 Topic for the hackathon of March 2023 Ready for Review update module
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Prodigal: zip output
3 participants
@kedhammar @SPPearce @maxulysse