Sequana

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MAJOR release merging the rnadiff branch into the dev branch so as to
finalise the way differential analysis are handle in Sequana with respect to
RNA-seq analysis

Module concerned: rnadiff, compare, featurecounts and enrichment

* CHANGES:

* removed expdesign module. Improved iem module to cope with old formats. From
now on, we wil use IEM formats only for the illumina sample sheets. No more
home-made formats will be supported.

* NEWS:

* module kegg and command in sequana (sequana taxonomy) to search for a given
name in all KEGG orgnanism so as to easily retrieve the taxon and organism name

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* BUGS:

* fastqc.FastQC class can now hndle empty samples (no reads... yes it may
happen)
* fastq random read selection corrected to handle paired data

* IMPROVEMENTS:

* CLI sequana summary can parse GFF and print summary information
* add custom section for Makefiles in pipelines
* add an unlock.sh for all pipelines
* featurecounts: allow input to use the --extraAttributes option; more tests

* NEWS:

* gff 1. add save_gff_filtered method to select interesting features, 2. add
gff2gtf conversion
* fasta module has GC content method
* new rule macs3_dynamic

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* rnadiff HTML report can now show the locus_tag in volcano plot
* rules star_index uses floor instead of round for small genomes to agree with
star index recommandation
* add MultiFeatureCounts() class to read several feature counts

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* BUGS:

* Fix star_index rule (regression bug) reported in https://github.com/sequana/sequana_rnaseq/issues/7


* IMPROVMENTS/CHANGES:

* add plot() method in Repeats class
* featurecounts: sort the output dataframe columns
* sequana CLI: summary/enrichment sub command allows to switch
between log/linear scale + option to compute the GO levels and
empty plots are now shown

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* rules fastqc: allows handling of bam files. remove sanity checks on empty files.
* rules falco: new rules added (similar to fastqc)
* module snaketools: PipelineManagerGeneric set paired field to "undefined"
since this is suppose to deal with bam, or other non-fastq files
* module fastqc now plots the pacbio phred score on the full y-axis range
* for developers: In SequanaManager teardown, option to skip check_fastq_files

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* faster gff module to be used by sequana_rnaseq>=0.9.19