I've used MicroHapulator to analyze single-end data from the Ion S5 before. However, this was before the end-to-end mhpl8r pipe command had been implemented. The end-to-end workflow provides numerous convenient and interactive tables and figures, and users with single-end data will no doubt want these features as well.
This PR updates the mhpl8r pipe command and associated code for single-end support. Most notable changes include the following.
Added a --single flag, which must be used to indicate single-end data inputs; by default paired-end data is assumed.
Created a new microhapulator/workflows/ directory, moved microhapulator/Snakefile to microhapulator/workflows/analysis.smk, and placed pre-processing rules in microhapulator/workflows/preproc-paired.smk and microhapulator/workflows/preproc-paired.smk.
Make changes to the pipeaux module and the HTML template to support conditional data collection and rendering. (I want to go through this code again before review.)
Closes #144.
[x] Changes are clearly described above
[x] Any relevant issue threads are referenced in the description
[x] Any new features are tested (see the development manual for details)
I've used MicroHapulator to analyze single-end data from the Ion S5 before. However, this was before the end-to-end
mhpl8r pipecommand had been implemented. The end-to-end workflow provides numerous convenient and interactive tables and figures, and users with single-end data will no doubt want these features as well.This PR updates the
mhpl8r pipecommand and associated code for single-end support. Most notable changes include the following.--singleflag, which must be used to indicate single-end data inputs; by default paired-end data is assumed.microhapulator/workflows/directory, movedmicrohapulator/Snakefiletomicrohapulator/workflows/analysis.smk, and placed pre-processing rules inmicrohapulator/workflows/preproc-paired.smkandmicrohapulator/workflows/preproc-paired.smk.Closes #144.