I11 - Add a general Email module

[jsbrittain]

Module can be used to send emails at various stages of a workflow. Credentials are provided by local file, and email transmission is triggered by the presence/arrival of a trigger-file which can be user configured.

To test the module:

• Pull down this branch
• Create a 'results/credentials/credentials.json' file (in accordance with the workflow/Snakefile docstring); note that this replicates a separate module which would like to a local file during normal execution.
• run snakemake --use-cores 1 --use-conda

To test the module in grapevne:

• Obtain and build the latest version of GRAPEVNE
• Pull down this branch
• redirect grapevne to the workflows folder in this repo (use the local copy, since the module had not yet been merged in)
• connect the module to some Local file modules in order to provide credential and trigger files.

[jsbrittain]

I've updated the module to permit glob-matched email attachments, and to support monitoring of successive email 'triggers' to permit multiple sends (these are useful when monitoring long jobs); there is a test config file with short timeouts that can be run as snakemake --cores 4 --configfile config/config_test.yaml.

[jsbrittain]

Squashed the last two commits to remove email from the commit history.

[jsbrittain]

I know this has already been squashed and merged but I have added two relatively minor comments and, also, try as I might I can't get it to work in GRAPEVNE

@rowannicholls Thanks for taking a look at this - I think you've found an issue that was initially overlooked. Although everything seemed to work on my test-bed, trying it on a clean install did raise an unexpected issue when testing in GRAPEVNE (the email standard library module was not being bundled with the packaged python/snakemake environment). I will add this to the new PR.

In the meantime (and just for clarity) to test the module in grapevne:

• Follow the setup instructions in the Email module's docstring to create an 'app password'. You will need the username and password saved into your credentials.json file.
• Use the LinkLocalFile module to provide the credentials file to the Email module.
• Connect the same LinkLocalFile module to the 'send' port (you can use it as a trigger by changing the 'send email' trigger filename in the Email module paramers, or use the new Touch module)

Here's a screenshot of my setup: