~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* BUG FIXES:
- sequanix:
- rulegraph issue on SLURM system. Avoid the os.chdir
- fastq_samples/ fastq module: fix histogram_gc_content maximum range
- rulegraph rule: fix issue 405 (spaces in path to snakefile)
- genome coverage was buggy for multi chromosome and circular option on. Fixed
- adapters/expdesign modules: fixe the case of design files with same sample
name and same index but different lanes.
- sequana_coverage. Fix Issue 416 (float division by zero)
* CHANGES:
- sequanix:
- snakemake output is now cleared when pressing RUN
- quality_control pipeline: default to atropos instead of cutadapt for
adapter trimming. Kraken: remove classified reads and keep
unclassified. Unclassified reads are now compressed.
unclassified reads that are also compressed now.
* NEW:
- pacbio module: cleanup and add funcion to convert input BAM into Fasta
- sequence module: Repeats class added
- new Snakemake pipeline called qc_pacbio to perform quick QC and taxonomy analysis
for pacbio
- add ORD, CDS, GC SKEW in sequence module.
0.2. - March - April 2017
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* NEWS:
- RNA-seq pipeline added (single-end only, paired-end upcoming)
including all indexes for RNA-seq
- Hierarchical kraken available
- add new standalone called **sequana_fox** to expose the pyqt5 browser.
- Sequanix first release
- final version of the variant calling, denovo, quality_control and rna-seq
pipelines.
* CHANGES:
- Sequanix/Sequana:
- config file can have the yml extension (in addition to yaml)
- dropdown widgets in the form based on the docstrings in the config file
- can import config to override default sequana config file
- subprocesses killed when the main pipeline is stopped