HTStream needs more informative logs

s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

https://s4hts.github.io/HTStream/

Apache License 2.0

49 stars 9 forks source link

HTStream needs more informative logs #175

Closed samhunter closed 4 years ago

samhunter commented 4 years ago

To help with the reproducible research problem, bioinformatics apps should be logging version, parameters, and as much other pertinent information as possible (see https://twitter.com/mikelove/status/1206202957370417152). This should be easy to add in the HTS logs. Some things to log could include: version, and maybe full path to exe, command line parameters, working directory, date and time, full path to input files (or "stream"), and maybe more?

msettles commented 4 years ago

branch reproducability (Ya horrible name) is meant to do a lot of this but I'm struggling to get the command line recorded into the json file, boost::any isn't easy to type cast our large argument set

msettles commented 4 years ago

Pretty much all handled in #189 at least keep all the command line options and version in order to recreate