Skip to content

Stand-alone metatranscriptomics worflow implemented
Compare
Choose a tag to compare
@iquasere iquasere released this 24 May 10:21
· 179 commits to master since this release
1.6.0
0b15425

Metatranscriptomics can be used as reference without metagenomics

  • If MG is not inputted, MT will be used for the MG part of MOSCA's workflow - assembly, binning, gene calling and annotation.
  • Trinity and RNAspades now available as assembler options
  • rule join_reads now considers possibility of MT as reference

Changes in config.json

  • experiments.tsv integrated into config.json as a parameter (list of dictionaries)
  • adapted config.json column names to MOSGUITO
  • New parameter - "suffix"
    • This parameter allows to specify a suffix to follow the _R1/_R2 special characters in files names, MOSCA will consider that those characters are followed by the "suffix" (e.g., _L001 would serve for the files mg_R1_L001.fq and mg_R2_L001.fq)

Adaptations for new versions of tools

  • SortMeRNA 4 fully implemented
  • Always gzips SortMeRNA output
  • UPIMAPI used directly instead of DIAMOND
    • MOSCA now accepts UPIMAPI's three options for database: "taxids", "uniprot" or "swissprot"
  • Small adjustment on CI to allow running reCOGnizer with mini cdd.tar.gz
  • Fixed krona version (to 2.5) for compatibility with MaxBin2 - MaxBin2 dependencies are presenting problems for higher versions, and krona's more recent versions would force to install those damaged dependencies

Added technical files, removed old scripts

  • added .gitignore
  • join_information.py deprecated, replaced by mosca_tools functions and rules in Snakefile

Changes in environment and CI files

  • install.bash no longer installs mamba
  • added gmcloser to environment.yml
  • added simplified cdd.tar.gz for CI
  • added test for complete workflow of MOSCA
  • new default for max-ref-number with metaquast - is now 0 to allow running CI

Miscellaneous fixes

  • fix on snakefile - checks if "Name" in "experiments" is ""
  • bins and DE results go to the folders of their respective "samples"
  • several fixes on reporting
  • fix on alignment functions in mosca_tools.py
  • fix on de_analysis.R
  • fix on obtaining directories for Illumina adapters and rRNA databases on preprocessing step
Assets 2
Loading