Sequana

Latest version: v0.18.0

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0.1.19

~~~~~~~~~~~~~~~~~~~~~~~~


* CHANGES:

- misc module: factorise on_cluster() function used in compressor scripts to
be used in other tools such as sequanix
- compressor: limits max number of jobs to 20 (can be bypass manually),
prevent run on TARS if snakemake-cluster not provided.
- rules:
- dag: now the snakemake is called inside a temporary directory to avoid
clash with the current snakemake process. This avoid error message.
Fixes https://github.com/sequana/sequana/issues/331
- __init__ was optimized as well as many modules to make use of the lazy
import mechanism. The reporting package is not part of the exposed module.
So::

from sequana import BAMReport

is now::

from sequana.reporting.report_bam import BAMReport

* NEWS:

- Sequanix stable version
- add TrueSeq adaptors
- add lazy import mechanism to speed up the time to import sequana, which
speeds up the --help in the standalone

0.1.17

~~~~~~~~~~~~~~~~~~~~~~~~

: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
----------

0.1.16

~~~~~~~~~~~

* BUG Fixes:

- Fix sequana_taxonomy (https://github.com/sequana/sequana/issues/308)
- Fix typo in sequana_coverage for multiple chromosome (https://github.com/sequana/sequana/issues/307)

* NEWs:

- SequanaConfig can read back a SequanaConfig instance
- Added a DummyManager for minimalist manager to create reports

0.1.15

~~~~~~~~~~~

* CHANGES:

- coverage: https://github.com/sequana/sequana/issues/302
add histogram, better stats table. add --output-directory
- Update docker (add bowtie, subread, firefox)
- snaketools:
- empty strings are kept as empty strings (not None)
- remove check() method in SequanaConfig
- cleanup (removing of templates) ca be switch off

0.1.14

~~~~~~~~~~~

* CHANGES:

- fastqc.histogram_sequence_lengths (log2 scale to log10)
- multi_summary fixed and available for the quality_control pipeline
- sequana_compressor: add --keep-going option by default so that if a file
fails, other independent files are processed.
- snaketools:
- remove SnakeMakeProfile (not used)
- remove sequana_check_config (not used)
- remove deprecated __get_tagname
- remove ExpandedSnakefile since not required anymore
- Fix sample_file2 option that was not encoded properly
- PipelineManager and SequanaConfig use new yaml parser
- sequana_coverage: -- add back the sample name as prefix of the HTML report
name -- a BED with two coverage columns is now accepted --
--download-genbank option added
- sequana_summary works for the quality_control pipeline
- Simplify combos of input_directory, input_patter, input_samples, the new
possible mutually exclusive input parameters of sequana standalone and all
pipelines.

* BUGS:

- Kraken: if no reads classified at all, errors were raised and
quality_control summary report would fail. This is fixed now with a "nodata"
image being shown.

* NEWS

- GUI (draft version)
- fq.gz are now allowed in the pipelines and should be supported in the
future
- More tests in particular a ./test/pipelines/ new directory

0.1.13

~~~~~~~~~~~

* CHANGES:

- revisited all pipelines so that they can work of multi samples.
- quality_phix, quqlity and quality_taxon pipelines merged in
quality_control pipeline
- running meadian won't fail anymore with odd window size (we add +1)
- rulegraph is used as well as dag to create figures of the pipelines

* NEWS:

- compressor: includes dsrc format in addition to bz2 and gz
- snakemake rule extension for sphinx
- add a pipeline manager in snaketools to handle all pipelines
- a designexp module to handle adapter design files

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