things_to_add

To-Add:

• Log Files -> where are they? what are they?
• Output File -> where are they? what are they?
• Cutadapt script
  • how does the detection of primer work?
  • what are the parameters I use for cutadapt?
• add what is in Hake_2019_metadata.csv?
  • bc that is necassary for people to make themselves if they're using new data/new primers
• make templates for csv's for new primers
  • primer_data.csv
  • Hake_2019_metadata.csv
  • known hashes.csv
• I'm using non-MURI data/new primers! A guide
  • kinda like a checklist to do before you start the pipeline if you have new data or primers
• Small Test dataset (DL and MFU)

Done:

• Docker instructions
  • instructions for both singularity and docker
  • docker instructions for mounting data
• Home page
  • table of contents
  • pipeline infographic
  • general overview of the pipeline
• Dependencies
  • R script that installs R dependencies for you
• DADA2 script documentation
  • added explanation of qual trim algorithm
  • linked DADA2's tutorial for general steps