Sequana

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

* BUGS:

* Fix regression bug (https://github.com/sequana/sequana/issues/484)
* Fix missing N_final column in table of the quality_control multi-summary
page
* Remove phix174.fa requirements in RNAseq pipeline config file
* Fix path starting with tilde (https://github.com/sequana/sequana/issues/486)

* NEWS:

* add isoseq Class
* add vcf_filter module back to help in filtering VCF files created with
mpileup for instance
* add sequana_vcf_filter standalone
* add cigar module to help deciphering CIGAR strings

~~~~~~~~~~

* BUGS:

* pipeline quality control: fix https://github.com/sequana/sequana/issues/477
* Fix empty dependency list in HTML report if sequana installed with conda

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

* BUGS:

* add missing file for the RNAseq pipeline in the setup.py
* Fix RTD building
* Fix reag_tag filtering https://github.com/sequana/sequana/issues/480
* Set singularity hub (v2.4)

Prior 0.5.X
-----------

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

* BUGS:

* cutadapt rule: remove the '--progress bar' for now because of a bug in atropos
(reported) that fails in the progress bar code

* Updates:

* pipeline pacbio_qc: finalise output tree structure.
* pipeline quality_control: add sanity check (thread must be >1 for
atropos) and run fastqc on unmapped data (rather than mapped).
* pin atropos version to 1.1.10 and added to requirements.txt
* Fix parsing of atropos report
* Update FastQC significantly to use atropos FastqReader instead of pysam.FastxFile
* documentation for the installation (remove docker, add singularity)
* rule/module atropos: implement ability to parse json report from atropos
https://github.com/sequana/sequana/issues/448
* rule fastqc: the log is now a variable. all pipelines using this rule
have been updated to save the log in {sample}/logs/ intead of ./logs
* add polyT in TruSeq adapters

* News:

* add Singularity container
* BAM class (bamtools module): add plotting methods (coverage, letters,
indels)
* Add Cigar class (cigar module).
* Sequanix: add option to switch on/off the tooltips
* rule cutadapt: (1) check whether thread is set to > 1. if not set to 2
(2) add --report-format to save reports in JSON and TXT

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

* BUGS:

* Set -t thread options correctly in the different rules (e.g. cutadapt)
* pipeline variant_calling: fix the VCF inputs when snpeff is off .
See https://github.com/sequana/sequana/issues/471
* pipeline quality_control. Fix regression bug introduced by the use
of sambamba in the bwa_mem_dynamic rule (see
ihttps://github.com/sequana/sequana/issues/472)
* Fix wrong total bases values in summary report of the quality_control
pipeline computed in FastQC class (see
https://github.com/sequana/sequana/issues/470)
* pipeline pacbio_qc: hard-coded the number of threads to 4 otherwise may
fail on clusters. Does not change the pipeline or analysis itself
* sequana_coverage: fix chromosome option.
* Fix genbank_parser when the genbank contains several concatenated genbank
entries. This fixes the coverage reports CSV file that had missing
annotations.
* Fix regression bug introduced in rule bwa_mem_dynamic that messed
up R1 and R2 order as compared to samtools by using sambamba. Fixed by
using -N parameter.
* Fix the -p option to be before the input whenever pigz is used in a rules.
Indeed -p may be ignored otherwise e.g. on clusters.

* Updates:

* add pacbio option in the mapping code
* pacbio_qc: fix pattern to filter input BAM files
* Speed up fastq_count (https://github.com/sequana/sequana/issues/465)
* bamtools module: speed up initialisation. add is_sorted method.
* bedtools: limit number of points to 1,000,000 in plot_coverage and set
ylimits manually to 6 mean coverage. add __eq__ function. See 464 issue
* Repeats can handle FastA properly (not limited to first sequence anymore)
* sequana_mapping: add thread in samtools call

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

Tag a stable release