Lex Nederbragt

Plotting the entire figure using a notebook. Work in progress. I would appreciate input on how to increase the resolution of the thumbnails of the instruments...

How to deal with the message about how to perform `git pull`?

6

Recent versions of git show this message after a `git pull`: ``` hint: Pulling without specifying how to reconcile divergent branches is hint: discouraged. You can squelch this message by...

https://github.com/carpentries/workshop-template/wiki/Configuration-Problems-and-Solutions#python still mentions IPython notebook and Canopy.

In `index.md` it is written "large-print handouts are available if needed". So far I have not been able to find them. On Slack it was suggested to use Chrome for...

Add locations of true and false positive variant calls

2

As per #25: > explain how to inspect alignments to see whether a variant is indeed called correctly, maybe point to a variant that did not pass filtering This requires...

In `04-units`, it would be good to add a test for an empty list - unless it is too advanced to test for catching exceptions?

Manual: use `from to:` to include parts of other doconce files

1

Add the new feature mentioned in #43 into the manual (at least I can't find it and I really like/need it!)

Demonstrate effect of conda activate

1

In `02-working-with-environments`, around the first time `conda activate` is run, it would be beneficial to demonstrate the effect of the command by something like: * run `$ python` (to get...

use of `./env` may be confusing

1

in `03-using-packages-and-channels`, the command `conda install tensorflow=1.14 --channel conda-forge --prefix ./env` uses `./env` as folder name. At the workshop today, this confused learners as they used had learned about `conda...

Strand bias of errors is an interesting aspect of read QC. It should not be too difficult to add something to preqc that measures/quantifies this (he said naively)...