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TODO.md

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TODO list

  • Check if names are unique, this is important for funannotate compare and probably also relevant in general.

  • add genome summary script as alternative to funannotate compare

  • add option to run with Docker or Singularity

  • Clean data.csv file (some fields are redundant)

  • add check when --setup is run again.

  • remove batch number check when annocomba --setup is run

  • hack augustus to recognize lower case repeatmasked files for auto training

  • fix augustus parallelisation hack

  • make sure assemblies are found both when specified with relative and absolute paths

  • check presence of interproscan during setup

  • check presence of genemark key file during setup - do dummy genemark run to check that key isnt expired?

  • modify annocomba setup part to read in paths to maker, repeatmasker, funanotate, genemark, eggnogg, genemark, interproscan and only run the respective setupp rules if present

  • make repeatmasker setup a separate rule and allow repeatmasker setup also if no repbase db is provided (need to change bin/setup_Repeatmasker.sh)

  • make antismash in rule remote optional

  • make busco rule more verbose when busco_set is missing. Right now the whole pipeline slowly fails after a failed busco rule

  • pipeline crashes when no protein evidence is provided in data/protein_evidence

  • perhaps it would be better to change the structure of the repo so that when cloned you already get the basic directories in data/ (assemblies, external, etc.), rather than have these in .gitignore, have .gitignore in the directories that ignores all in the respective directory

  • Re. change Repeatmasker to lowercase. Repeatmasked fasta is used by Augustus. I forgot about that. Need to adjust augustus command and add --softmasking=1 so that the softmasked repeats are interpreted correctly. Will have to change the augustus call in the code of autoPred.pl.