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.

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

Prepare a tidy results file #17

Merged
merged 18 commits into from
Oct 30, 2023
Merged

Prepare a tidy results file #17

merged 18 commits into from
Oct 30, 2023

Conversation

adamjtaylor
Copy link
Collaborator

@adamjtaylor adamjtaylor commented Oct 19, 2023

The results.tsv output by HistoQC has a number of quirks including header rows and the possibility of tabs existing within columns. This makes the results.tsv not ready for display in Tower Reports or to upload as a Synapse table, and somewhat confusing to parse as in pandas or similar.

This PR adds a module to transform the results.tsv into a tidier results_tidy.csv

  • Add pandas to nf-histoqc Docker image (currently uses container from nf-artist) - or use a minimal container including pandas

@adamjtaylor adamjtaylor self-assigned this Oct 19, 2023
@adamjtaylor adamjtaylor merged commit fa53aa7 into main Oct 30, 2023
1 check passed
@adamjtaylor adamjtaylor deleted the tidy-results branch October 30, 2023 19:32
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant