* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
* Update LAST to version 1238.
* Update functions.nf to the latest devel version.
* Update test MD5sums after updating software version.
* Make portable on MacOS
* Allow input alignments to be uncompressed.
While the strategy in this family of modules is to make all inputs and
outputs compressed, this change might be useful to some users.
As of LAST 2138, `last/split` does not allow its input to be compressed.
* Search for .des file, that is guaranteed to be unique.
Some LAST indexes have more than one .bck file and it makes the name
detection crash.
In this commit, I also standardise how the names are detected.
* Use value input channel and optional output channels to handle formats.
As discussed on Slack, it is preferred to use a value input channel
instead of sneaking options through `params.args2` or `params.format`
as we did.
Likewise, optional output channels with clearly labeled format are
preferred to 'catch-all' wildcards.
* New last/dotplot module for pairwise similarity plots
The `last-dotplot` tool takes a pairwise alignment in
[MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format,
possibly compressed with gzip, or in a tabular format produced by the
`maf-convert` tool, and produces a similarity dot-plot of the two
sequences in one of the graphical formats supported by the Python
Imaging Library.
A the tool guesses the output format by the file extension of the file,
which is constructed by the module at run time, I have used the `args2`
option to convey this information to the module.
This new module is part of the work described in Issue #464. During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence please ignore lint's version warning).
* Update the functions.nf file to the dev branch.
https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
