Releases: JasperBoom/caltha
Releases · JasperBoom/caltha
Caltha 0.6
Version 0.6
Current stable version. Previous versions should be ignored.
- Add
pytest
file presence test function for regular fastq file input. - Add
pytest
file presence test function for gzipped fastq file input. - Add
pytest
file presence test function for regular fasta file input. - Re-add
pytest
test file with file presence test for gzipped fasta
file input (further tests will be added later). - Remove both the umi sequence and the centroid sequence from the tabular
output, as requested by users and noted in
(issue 7)[https://github.com//issues/7]. - Fix fasta file creation, where new read headers would not start on a
new line, but append to the sequence of the previous read. - Rename
PreZip
folders and files toPreValidation
. - Fix bug where umi count would be reset to 1 for every read.
- Replace reverse complement function with the
biopython
Seq class. - Add
pyfastx
for the parsing of the fasta/fastq files (which also adds
support for single gzipped input files or multiple gzipped files in a zip
archive). - Update documented python version to 3.8.
- Rename variables in core script and update
Caltha
--help
page. - Update README.md & index.md to reflect current project state.
- Fix
pre-commit
files.
Caltha 0.5.1
Version 0.5.1
- Restructure versioning to match PyPI package.
Caltha 0.5
Version 0.5
- Setup
pre-commit
withBlack
andFlake8
.
Caltha 0.4
Version 0.4
- Add code style
Black
.
Caltha 0.3
Version 0.3
- Updated python script for umi5 primer single test to work with parallel
processing. - Added zip file for umi5 primer multiple test.
Caltha 0.2
Version 0.2
This release of Caltha
implements parallel processing. This parallel
processing only has effect when multiple input files are provided. Caltha
now
allows a .zip file with either fasta or fastq files as input. The output has
been changed to three zip files, one for the tabular files, one for the pre
validation zip files and one for blast files.
- Added
parallel processing
issue #2. - Added
.travis.yml
configuration file.
Caltha 0.1.3
Version 0.1.3
- Added python script for umi5 primer single test.
Caltha 0.1.2
Version 0.1.2
- Added fasta file for umi5 primer single test.
Caltha 0.1.1
Version 0.1.1
- Implemented a umi length check.
Caltha 0.1
Version 0.1
First release on GitHub for the new Caltha
tool.
Any changes mentioned below were applied to the main python script after it was
isolated from the old "galaxy-tools-umi-isolation" repository. This python
script is now a package on PyPI and will be maintained in this repository.
- Created PyPI package for
Caltha
. - Added documentation page to repository (still needs to be filled).
- Zip archives are now created
byCaltha
(used to be created by a BASH script). - Temporary working directories are now managed by Caltha (used to be managed
by a BASH script). - Wrongly assigned reads bug was
fixed (PR by https://github.com/dickgroenenberg). - Renamed
galaxy-tools-umi-isolation
python tool toCaltha
. - Isolated
galaxy-tools-umi-isolation
python script to dedicated repository.