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This is an stable release made to includes lots of new features and pipelines
and bug fixes made.
We removed all pipelines from sequana. Pipelines have now their own repositories
on github to ease the developpement of sequana and those pipelines. The
rationale being that we do not need to update sequana when a pipeline changes
and a pipeline can have its own biocontainer and life cycle. We kept just one
for testing purposes (compressor). Other pipelines have now their own repositories:
- sequana_coverage
- sequana_demultiplex
- sequana_fastqc
- sequana_revcomp
- sequana_rnaseq
- sequana_variant_calling
- sequana_denovo
- sequana_pacbio_amplicon
- etc
New pipelines have been added such as sequana_downsampling and sequana_mapper.
* NEWS:
* snpeff now includes GFF input file input as an option (in addition to
the GBK)
* new module trf for tandem repeat finder output.
* new scripts:
* sequana_start_pipelines to initiate a new pipeline from the cookiecutter recipes
* sequana_gtf_fixer to help fixing GTF issues
* new module *gff3* to read GFF files
* Module can now encapsulate logos
* Module version implemented
* BUG:
* snpeff_add_locus_tag: if contig name and length in GFF header not in the
same order as in the fasta, a new fasta with wrong header was created.
This caused trouble in the variant_calling pipeline
* kraken: Fix kraken plot (matplotlib version) when 100% of the reads are
classified
* Header of igvtools count output may vary. Make the consensus.get_bases more
robust to automatically identify number of lines to skip.
* Fix the kraken multiqc report
* Fix bug in gui/browser to fix import of QWebPage on travis
* bowtie2 dynamic rule now uses templating correctly (RNASeq pipeline)
* Fix issue in snaketools for input_readtag set to _[12] for paired data
The paired attribute wass wrongly set to unpaired. Besides, we make it
more robust for those who tag their paired data with _1 and _2 instead of
_R1_/_R2_
* Repeats: for multi fasta with similar header, we were expecting the chrom
name to be unique but underlying tool uses regular expression. So, this was
buggy when chrom name were starting with same string. e.g chr1 anc chr11.
* multiqc section of sequana_coverage: duplicate chrom names across multiple
samples were shown as a single entry in the report.
* draft version of multiqc for sequna_quality_control now available
* MAJOR CHANGES/FIXES:
* The main script 'sequana' is redundant with the new framework of
pipelines. It has been removed in this version
* sequana_coverage now handles low coverage correctly in the
HTML reports.Fix the ylimits of the coverage plot for low coverage.
* cutadapt rules was failing due to a stricter optional/positional argument
handling. Fixed the rule accordingly.
* sequana_lane_merging is now ready for production. changes made: copy of
the script in the local directory, not the data directory.
* RNASeq pipeline: removed sartools, kraken. Fixed bamCoverage rule. Simplify
usage related to indexing and mapping. Fixed igvtools rule. Fixed the
reoderSam rule (wrong executable). Fixed a incorrect parameter name in
bamCoverage rule. Fixed incorrect Snakemake syntax in the fastq_screen
rule and RNAseQC. Fixed another deprecated rule: fastq_screen_report.
* New pipeline_common module to be used by all pipelines
* MINOR CHANGES/FIXES
* snaketools:
* pipelines discovery updated in ModuleFinderSingleton. Finally
fixed the lost of comments in the config when saved.
* Removed onweb() method.
* Fixed the loss of comments when saving yaml file after an update
of the key/value.
* remove check_sequana_fields.
* more tests and cleanup
* demultiplex: fix a Pandas deprecated warning (add sort argument in pd.concat)
* python dependencies not in conda are not harcoded inside the setup.py
(itolapi). add cython into the list of requirements.
* Fix deprecated bamCoverage rule to use newest deeptools version.
* The check_config_with_schema function now performs the validation
correctly
* Fix stdout of the fastqc, unpigz, bowtie1 and bowtie2 rules
* Atropos 2.0 changed its API. fastq module compat with atropos 1.0 and 2.0