Sequana

-----

general
~~~~~~~~~

* finalise the rnadiff HTML report with plotly visualisation
* finalise the enrichmentf HTML report
* template for rnadiff (rna differential analysis)
* method in FastQ to extract some specific reads
* add new application in main sequana tool:
- biomart: a tool to produce a CSV for a given dataset!mart/set of attributes
- summary: a tool to produce HTML for bam, fasta/fastq/bam, rnadiff results, enrichment for a rnadiff result
- fastq: can now merge several files
- gtf_fixer that replaces the script sequana_gtf_fixer
* add quick_fix for sample sheet errors in iem.IEM class (used in
sequana_demultiplex pipeline)
* Fix featurecounts package to include tolerance parameter
* Fix bug for category in Dendogram

for developers
~~~~~~~~~~~~~~~

* rules: star_index now sets automatically the IndexNbases parameter
* removed sequana_summary from standalone now in the general sequana CLI
* improved find_motif module with plots, pep8, better API
* js: reverse papaparse

-----


* add salmon module for the rnaseq pipeline
* fix bug in multiqc plugin for bamtools used in sequana_mapper
* some rules updates: (1) add_read_group has now the option
"VALIDATION_STRINGENCY=SILENT" that seem to be required in newer version of
picard. surprising that this error did not appear earlier since the issue seems
old (https://github.com/Cibiv/NextGenMap/issues/3) (2) mark_duplicates and
features_counts rules needed o change some parameters, now keywords in snakemake
* add new viz module called dendogram
* add new report module for rnadiff.
* add new report module for KeggPathway and Panther
* Add solution to convert ensembl ID to gene name fr the KeggPathwayEnrichment
* Sequana main script has now a 'summary' command. Integrated the RNADiff and
BAMQC modules for now.

-----
* Fix html syntax in the templates
* Fix demultiplex.barplot_samples layout
* Created a sequana main script with currentl one command, fastq, which replaces
sequana_fastq_head, sequana_fastq_count, etc

-----


* Fix requirements (missing stattmodels)
* Fix bug kraken sequential when no reads are classified
* Fix FileFactory to make it much faster (speed up pipeline initialisation). This should also fix a recurrent issue with read tag (see https://github.com/sequana/sequana/issues/526
* NEWS:

* implemented rnadiff module
* implemented go term enrichment
* implemented feature counts
* implemented plot.viz.venn
* implemented compare module (for rnadiff comparison)

-----

* CHANGES:

* module kraken: better label in plot2 method to avoid long label to be cut
* module compare: fix label in comparative plots
* module modules_report/bases now include title in the embedded image

------

* CHANGES:

* coverage multiqc plugin to remove unique chromomosome name from the sample name, if it is unique
* bamtools_stats multiqc plugin to remove unique chromomosome name from the sample name, if it is unique
* fix regression bug in report summary page for the taxonomy tools

* NEWs:

* Contigs now acceps Spades fasta files
* added a new viz module for PCA plotting
* added a new stats module for data normalisation
* added a new enrichment module to include KeggPathway enrichment