- rulegraph issue on SLURM system. Avoid the os.chdir
fastq_samples/ fastq module: fix histogram_gc_content maximum range
rulegraph rule: fix issue #405 (spaces in path to snakefile)
genome coverage was buggy for multi chromosome and circular option on. Fixed
adapters/expdesing modules: fixe the case of design files with same sample name and same index but different lanes.
sequana_coverage. Fix Issue #416 (float division by zero)
- snakemake output is now cleared
- quality_control pipeline: default to atropos instead of cutadapt for
adapter trimming. Kraken: remove classified reads and keep unclassified. Unclassified reads are now compressed. unclassified reads that are also compressed now.
pacbio module: cleanup and add funcion to convert input BAM into Fasta
sequence module: Repeats class added
- new pipeline called qc_pacbio to perform quick QC and taxonomy analysis
add ORD, CDS, GC SKEW in sequence module
- RNA-seq pipeline added (single-end only, paired-end upcoming) including all indexes for RNA-seq
- Hierarchical kraken available
- add new standalone called sequana_fox to expose the pyqt5 browser.
- Sequanix first release
- final version of the variant calling, denovo, quality_control and rna-seq pipelines.
- Sequanix/Sequana: - config file can have the yml extension (in addition to yaml) - dropdown widgets in the form based on the docstrings in the config file - can import config to override default sequana config file - subprocesses killed when the main pipeline is stopped
- add sequana_debug_level function at top level to switch verbosity of informative messages (default is WARNING).
- add pacbio module #351
- quality control pipeline: atropos can be used in place of cutadapt #346
Running Median is 10 times faster #345
sequana_coverage: (1) –file1 alone was not working (2) automatically copy cluster-config in working directory and update runme.sh accordingly #342
- sequana standalone:
- handles cluster_config Snakemake option
- add error message when adapter name is incorrect
sequanix: the help dialog is now created inside designer and has a proper scrollable browser dialog. cluster_config Snakemake option is also handle.
Remove galleria JS lib and related files (htmltools)
sequana_coverage: add –logging-level option
- Fix #352 : allow gc window size to be even (warning is shown and +1 to window size)
- Fix # 354: cutadapt report that was mixing up R1/R2 trimming in the images.
- –output-directory in sequana_coverage was failing
- in coverage, centralness was buggy (regression) and use number of ROIs instead of the total base length #347
- Fix multi_report summary for single end case #349
- remove pyquickhelper dependencies and add a simple rest2html function in misc module.
- 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.
- 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
from sequana.reporting.report_bam import BAMReport
- 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
|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.|
- 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.
- 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)
- add rubicon adapters
- add ability to read JSON in SequanaConfig
- SequanaConfig can read back a SequanaConfig instance
- Added a DummyManager for minimalist manager to create reports
coverage: https://github.com/sequana/sequana/issues/302 add histogram, better stats table. add –output-directory
Update docker (add bowtie, subread, firefox)
- empty strings are kept as empty strings (not None)
- remove check() method in SequanaConfig
- cleanup (removing of templates) ca be switch off
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.
- 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.
- 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.
- 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
- 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
- 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
- Fix bug in cutadapt pipeline when there is no adapters. Force a dummy adapters (XXX) otherwise trimming is performed on read1 only
- compressor rule and script available.
- coverage annotation
- multiple_summary draft
- add a docker
- sequana_summary standalone
- sequana_mapping standalone
- Module has an overview field
- cutadapt report handles single-end tables. Fix the reverse complement adapter files for the paired-end case
- sequana_standalone: final version with stats
- sequana_coverage standalone
- de-novo pipeline
- Remove AdapterDB, a draft version that uses Kraken to detect adapters. Not relevant anymore
- config.yaml is now in each pipeline to have a simplified version
- sequana can known use single_indexed or multiple_indexed adapters, which are also provided within sequana (Nextera and PCR free cases)
- Release for production (quality_taxon pipeline)
- rule data added and used in phix_removal (fastq_sampling + raw data switch)
- kmer module
- sequana_taxonomy standalone
- reports are now in ./sequana/reporting
- MAJOR refactoring of report/ directories in all pipelines to make them independent from the temporary analysis, which can then be removed.
- Fix running median issue in bedtools (window size larger than contig size)
- KrakenDownlad class: download kraken_toydv from sequana/data repository or minikraken into a local directotry
- New method in FastQC to show ACGT content
- Genomecov renamed into GenomeCov
- Update main script significantly to create multiruns and handle adapters
- GC content and plot GC vs coverage added in GenomeCov
- sequana_data by default looks into resources/testing directory
- in fastq module: FastQC a bit faster andFastQRandom class removed
- add a moving_average function in misc module
- sequana_data was showing __init__ and __pycache__ as possible data sets
- databases: filelist as a list was not implemented
- in fastq.FastQ extra_head in gzip mode was missing the last row
- sequana_taxonomy standalone available (kraken + krona)
- sequana standalone available
- quality_taxon pipeline available
- module coverage for theoretical computations
- add gallery in the documentation
- module vcf_to_snpeff renamed as snpeff
- Fix bug in running median (shift)