xyflo

A nextflow pipeline for finding enzymes in metagenomes

Require Dependencies

Install Nextflow

curl -s https://get.nextflow.io | bash

Install nf-test

curl -fsSL https://code.askimed.com/install/nf-test | bash

Usage

nextflow run wf.nf --bioProjectId PRJNA732531 -resume
nf-test test tests/wf.nf.test

Design Notes

• Current comfort level : Poor

  • Groovy: Poor
  • Nextflow: Poor
  • Bash: Ok
  • WF: Ok
  • Docker: Poor
  • Help from ChatGPT: Poor
  • Language Server: Poor

• Download fastq file using https://github.com/nf-core/fetchngs ?

  • How to use it from my pipeline instead of using it from commandline?

• Manage files in bash or nextflow?

• Poor commenting in bash