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* Added check in visualization to throw error if feature only has one type. * Increase metaphlan2 and strainphlan task times for larger grid runs. * Added option for custom databases for 16s usearch/vsearch methods.
* Added WDL workflow. * Increased default strainphlan slurm memory request to allow for larger runs. * Change formatting of panphlan task command to allow for grid runs.
* Allow for single QC database (fix ratio table in wmgx vis). * Add target for strainphlan best tree if created with generic clade name.
* Fix error when running wmgx_vis with metadata for ec heatmaps.
* Added heatmaps for ecs to wmgx vis. * Changed functional profiling outputs to optional in wmgx vis. * In demultiplex script make the index file optional. * Add script to pull out reads mapping to metaphlan2 species by marker. * Add two utility scripts for renaming tables and fastq files to sample ids. * Add script to update anadama2 database with new files. * Add workflow burst script.
* Added isolate workflow. * Increase kneaddata tasks time/memory to allow for new kneaddata feature which reorders sequences. * Add option to use bz2 input files for wmgx workflows. * Update dada2 ASV taxonomy table to sync ASV ids.
* Remove the taxonomy from the picrust2 input file to resolve the int/str error.
* Add PICRUSt v2 option (now also included as a task for the dada2 method). * Update 16s workflow for python3 compatibility. * Modify extract_markers.py strainphlan task to use new folder naming convention (to work with latest metaphlan2/strainphlan packages).
* Change kneaddata tasks to work with latest version as to not overwrite final pairs output file. * Data2 workflow new options added: minoverlap and maxmismatch. * Require min length for cutadapt to prevent reads of zero length passed to dada2 tasks which will cause an error. * New option to allow wmgx workflow to just run panphlan.
* Default kneaddata (QC tasks) no longer use the rRNA database for filtering * Default kneaddata runs with trf to filter repeats * For database install, the metaphlan2 folder name has been updated to work with the latest metaphlan2 version * Users can now run without any filtering databases for kneaddata tasks * Users can now pass custom arguments to humann2 tasks
* Add option to provide a list of strains to run (instead of default of top 25 by average abundance).
* Add panphlan optional tasks to wmgx workflow. * Add ITS option to 16s workflow.
* Add colorbar for continuous data to PCoA plots.
* In 16s usearch/vsearch methods combine truncate and filter (needed for data sets that require more filtering). * Add option to bypass msa generation in 16s workflows.
* Add vsearch as 16s workflow option (now the default). * Add assembly as option to wmgx workflow. * Add fasttree task to 16s workflow. * Add dual indexing option to 16s and wmgx workflows.
* Add DADA2 16s workflow option. * Add option to bypass taxonomic profiling for the wmgx workflow. * Strainphlan option now selects top species by average abundance for profiling. * Add genera visualizations to both 16s and shotgun workflows. * Add average grouped metadata plots for relative abundance.
* Add metadata input option to wmgx and 16s visualization workflows. * Add multiple sequence alignment task for closed reference sequences to 16s workflow. * Include 16s data products in 16s report archive. * Update 16s visualization workflow to pull variables from data processing workflow log to write report introduction. * Add optional picard input files to 16s visualization workflow. * Add options to bypass quality control and functional profiling to wmgx workflow. * Improve error message in database install script printed when required dependencies are not found. * Add counter to track PyPI download stats. * Update dependencies to require anadama2 v0.4.0.
* Change the default size of heatmaps in reports based on format. Increase the size in pdf and decrease in html.
* Added utility to automatically install databases for each data processing workflow. * Reorganized shotgun output file locations so the products are stored with respect to the software used to generate them.
* Shotgun task names updated to include sample names. * Strain profiling was added to the shotgun data processing workflows. * Executables are tracked for tasks in the data processing workflows. * Tutorial data files were added to the examples folder. * Eestats table added to 16s report. * Discordant alignments are now allowed in qc shotgun tasks (kneaddata v0.6.1+ now required). * Removed intermediate output option added to shotgun data processing workflows to reduce output size. * Table of contents added to reports. * Added workflow information (ie commands, software versions) to reports. * Reports updated to allow for large numbers of samples. * Updated qc tables to use serial filtering to show serial filtering in report. * Added rna/dna norm to data processing and visualization workflows. * Refactored visualization input to use output of data processing to allow for more input files. * Rna/dna renorm script refactored to increase speed (minutes vs days). * Time/memory equations added for compute intense tasks. * Reorganizing and polishing of reports. * Allow for different template formats and report formats. * Allow for custom comtaminate databases in the shotgun reports. * Added archive generation to visualization workflows. * Allow for compressed 16s paired end files as input. * Allow for fasta shotgun files as input. * Initial 16s workflow added. * Initial visualization workflows added.
* Initial shotgun data processing workflows added.