finish at --end-alignment and start --from-alignment

[stiatragul]

Description of feature

In my experience working with AusARG data, the two parts of pipesnake that take the longest time to run is in estimating gene trees followed by multiple sequence alignment. I think there's a few benefit in allowing users to finish their after the alignment is done then start again --from-alignment.

The idea is users can take the alignment out of the pipeline and trim/correct them before restarting at --from-alignment.

As an example, I've downloaded the MAFFT output folder with all the alignments to assess the quality with SEGUL. I then decided to trim all alignments using ClipKit and error-correct with TAPER. The sample names and file format (.fasta) remain the same, so it should be compatible with the next steps in pipesnake

[IanGBrennan]

Ok, assuming I've got this right, it's essentially two additional options

1. --stage end_alignment which will terminate the pipeline after the initial MAFFT alignments are made. This should be easy to implement.
2. --stage start_alignment (start_from_alignment?) which will initiate the pipeline from user provided alignment files. This will require providing the path to the directory of alignment files.