Ability to give RedDog a file containing paths to all reads

[jhawkey]

It would be nice if the pipeline had the ability to take a file containing the paths to all the sequences that need to be run instead of a python list of sequences.

Some users need to subset reads from multiple different locations and are unable to use wildcards to do this, so are forced to make giant lists in the config file giving the path to each individual isolate. A possible solution to this is instead giving pipeline a text file that has the path to one read set per line, to prevent users having to copy and paste large lists into the config file.

[d-j-e]

Possible to do, but a fair bit of work for rare case - and 'cut and paste' from a text file isn't that hard... To make it easier to read, isolates can be added like this:

sequences = ["path/to/file/1/seqA_.fastq", "path/to/file/2/seqB_.fastq", "path/to/file/X/seqX*.fastq"]

where seqA seqB and seqX are three different isolates in three different folders

Will revisit idea after release.