* 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/train module to train alignment parameters.
The last-train command creates a parameter file that
will be used by last/lastal module for sequence alignment.
It takes indexed sequences and query sequences as input
and we use the metadata of both to create an id of the
parameter output file.
Submission of the LAST modules is discussed in more
details in the issue #464. For consistancy, we use LAST
version 1219 for this whole development and will upgrade later.
* Corrected files according to the nf-core v1.14 standards.
* Fixed function.nf file for the last-train module.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Find index name.
* Correct after the input channels were changed.
* Use double underscore as a name separator.
Single underscores can happen in ids, therefore, we would like to keep two underscores.
* Remove extra spaces.
* Fixed the passing of the "score matrix" line.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/last/train/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
