NOMERGE Setup full testdata #2

pinin4fjords · 2023-01-09T17:50:43Z

Just for visualising difference between branches to help with some debugging.

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 - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/differentialabundance 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 --outdir <OUTDIR>).
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).

…riables in test data

Add optional GSEA analysis, update modules, fix minor bugs

Jonathan Manning added 5 commits January 9, 2023 11:49

Update test_full.config for test data added by @WackerO

abc3c4e

Add flexibility to schema for inputs

62c372b

Add sample id parameter

2c1acb5

Pass samples variables to markdown script

15069da

Adjust markdown process to deal with fallout from space-containing va…

818bb6f

…riables in test data

pinin4fjords marked this pull request as draft January 9, 2023 17:50

Jonathan Manning added 16 commits January 9, 2023 20:10

Reduce redundancy in varaibles for plotting

db353b8

Update DESeq2 module for spaces fix now merged to modules repo

ba574c0

Merge pull request nf-core#33 from healx/add_gsea

a8b5678

Add optional GSEA analysis, update modules, fix minor bugs

Update modules for better space handling

c75828e

Merge branch 'dev' into setup_full_testdata

8ed4997

Temporarily install updated modules from PR branch

94b200b

Fix test_full.conf

266de3a

Correct parameter pass-through in modules config

54aa620

Fix minor issues with local GSEA chip-creating module

a48121c

appease eclint

3d1e647

Parameterise feature information fields used and pass through

e92b30f

Fix modules now they're updated centrally

6adb790

Generalise sample to observation

3f50f73

Remove test line

c938cbe

Tidy up module params

616428e

appease eclint

7feb840