C. Titus Brown
C. Titus Brown
it'd be great to have the params file written into the output directory. separately, it would be neat to compare the parameter file in the output directory with the parameters...
GATK best practices diagram ++
add the key four steps to the README, https://hackmd.io/ZCX_8yx4QLOExT7dCjK3zQ?view#Doing-things-%E2%80%9Cthe-workflow-way%E2%80%9D
we now have the basic assembly under CI (yay!), up through annotation. but I'm wary of adding too many more _execution_ tests on Travis, because they take real time and...
tracy teal pointed me towards the term "playbook", https://docs.ansible.com/ansible/latest/user_guide/playbooks.html - maybe we could say eel pond (or elvers, or whatever we call it) is a "playbook" for RNAseq processing.
it would be great to have both standard and customized execution of notebooks after a run! not sure how to make 'em conditional on the workflow run, but that can...
I spent a frustrating time debugging tabs vs spaces vs... a few thoughts: * allow yaml input * allow csv input * allow excel input (??) * provide a utility...
which is fine, but it means that if you are starting with un-gzipped data the output of `get_data` is incorrect because it links the ungzipped files to filenames that end...
The whole repo history is in the ~100 MB range, while the current master is only a few MB. This makes it unnecessarily slow to check out the git repo...
on a Jetstream m1.medium, second run of nema-test (so, all software installed etc. etc.) /usr/bin/time -v reported: ``` Command being timed: "./run_eelpond nema-test full" User time (seconds): 1637.94 System time...