* 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
* New module last/mafswap to reorder sequences in alignments
The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reorders sequences in alignment files in Multiple Alignment Format.
When run without command-line arguments, it will swap the target and the
query sequences. This is useful when turning a many-to-many alignment
into a many-to-one and then a one-to-one alignment in conjunction with
the `last-split` command (split, swap, split and swap again).
The LAST aligner outputs MAF files, but other tools also use this
format. As MAF files can be very large (up to hundreds of gigabytes),
the module expects its input to be compressed with gzip and will
compress its output.
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 ignore lint's version warning).
* Update MD5 sum.
Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of
an empty file compressed with `gzip --no-name`… This happened
because I forgot to update the config file after correcting the
module… sorry !
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change name as suggested in pull request.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
