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TODO
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### List of "ToDo"s to do them all when I have time to do them
##########
## Main ##
##########
[TODO] scripts/BacterialTyper:: Config module: All
[TODO] Fix and install MLSTar during installation
[TODO] BacterialTyper/modules/set_configuration.py :: All
[TODO] BacterialTyper/install_dependencies.py :: All
[TODO] BacterialTyper/install_dependencies.py :: check and install edirect NCBI
[TODO] BacterialTyper/extern_progs.py :: Add install dependencies
##############
## Modules ##
##############
[TODO] BacterialTyper/modules/MGE.py :: Fix SettingWithCopyWarning warning message
[TODO] BacterialTyper/modules/database.py :: ariba user databases provided
[TODO] BacterialTyper/modules/database.py :: NCBI_descendant
[TODO] BacterialTyper/modules/variant_calling.py :: All
[TODO] BacterialTyper/modules/assemble.py :: Generate more comprehensive statistics
[TODO] BacterialTyper/modules/ident.py :: Samples might not be assembly or might not be species information for some. Take into account
[TODO] BacterialTyper/modules/ident.py :: Fix summary report
[TODO] BacterialTyper/modules/ident.py :: Sum plasmid and chromosome statistics
[TODO] BacterialTyper/modules/ident.py :: Add information if multiisolates are detected
[TODO] BacterialTyper/modules/ident.py :: parse data according to database: bacteria, plasmids or user data or genbank data provided
[TODO] BacterialTyper/modules/qc.py :: Control FASTQC statistics for trimming
[TODO] BacterialTyper/modules/qc.py :: Control BUSCO statistics for discarding samples if necessary
[TODO] BacterialTyper/modules/profile.py :: Add information summarizing results for other databases
[TODO] BacterialTyper/modules/profile.py :: check if it works database_user.update_database_user_data in profile
##############
## Scripts ##
##############
[TODO] BacterialTyper/virulence_resistance.py :: Implement if a different database provided (!= CARD, VFDB)
[TODO] BacterialTyper/virulence_resistance.py :: Parse if a different database provided (!= CARD, VFDB)
[TODO] BacterialTyper/species_identification_KMA.py :: Implement if a different database provided for KMA
[TODO] BacterialTyper/species_identification_KMA.py :: Implement if database (user_data or genbank) provided.
[TODO] BacterialTyper/species_identification_KMA.py :: Download after n days passed?
[TODO] BacterialTyper/species_identification_KMA.py :: Test single end
[TODO] BacterialTyper/MLSTar.py :: Check time passed and download profile/sequence again if >?? days passed]
[TODO] BacterialTyper/MLSTar.py :: update_MLSTar_profile_alleles()
[TODO] BacterialTyper/MLSTar.py :: Add help MLSTar
[TODO] BacterialTyper/MLSTar.py :: Check genus spp option to get PubMLST profiles
[TODO] BacterialTyper/trimmomatic_call.py :: Implement new parameters for trimming given the quality check analysis
[TODO] BacterialTyper/ariba_caller.py :: Different databases provided
[TODO] BacterialTyper/ariba_caller.py :: Check what to do with single end when calling ARIBA
[TODO] BacterialTyper/database_generator.py :: Add mash for external data
[TODO] BacterialTyper/database_generator.py :: NCBI descendant
[TODO] BacterialTyper/database_generator.py :: provide preference to db2update (update_db_data_file)
#####################
### Visualization ###
#####################
https://pathogen.watch/
https://microreact.org/about
#####################
### Documentation ###
#####################
[TODO] BacterialTyper/multiQC_report.py :: Generate help and information message for MultiQC
[TODO] BacterialTyper/species_identification_KMA.py :: Generate help and information message for KMA (help_kma_database)
[TODO] BacterialTyper/trimmomatic_call.py :: Generate help and information message for trimmomatic
[TODO] BacterialTyper/modules/info.py :: Generate help and information message for project
[TODO] BacterialTyper/modules/MGE.py :: Generate help and information message for MGE module
[TODO] scripts/BacterialTyper:: Profile module: add help additional databases
[TODO] scripts/BacterialTyper:: Identification module: add description
[TODO] BacterialTyper/BacterialTyper/min_hash_caller.py:: help message
##########################
### WIKI/Documentation ###
##########################
https://github.com/9999years/argdown
http://docutils.sourceforge.net/rst.html
https://help.github.com/en/github/building-a-strong-community/adding-or-editing-wiki-pages
https://guides.github.com/features/wikis/
https://github.com/matplotlib/sampledoc
Generate docstrings using http://rst.ninjs.org/
## example report
https://github.com/tseemann/nullarbor
## CITATION of the software
https://zenodo.org/