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:Main NEWS: The GUI was completed and the current pipelines stabilised (RNA-seq,
quality control, variant calling). The test suite was switched from nosetests to
pytest, in particular to perform tests more eaasily on the Qt GUI.
* BUG Fixes:
- experimental design and adapters API simplified fixing a few bugs in the
process. Doc and tested finalised.
- Fix cutadapt rules, which was not filling the fwd and rev properly anymore
when using the design file.
- in sequana main script, --reference was used by quality_pipeline only.
Now, available for all.
- Fix the main script for the reference in variant calling pipeline.
* CHANGES:
- sequana_compressor: for conversion from e.g gz to bz2, use a pipe instead
of double IO. Updated docs and tests ready for production.
- sequana standalone:
- --pattern changed to --input-pattern
- --output-directory changed to --working-directory
- remove pipetools module (obsolet)
- GUI revisited with qt designer + can now also read any snakefile/config
file combo (not just sequana pipelines)
- RULES: adapters can now use adapter_type without a design (fwd and rev
gets filled automatically)
* NEWS:
- add rubicon adapters
- add ability to read JSON in SequanaConfig
2016
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