05_nf-core_and_methylseq.md

SEMINAR 5: Introduction to the nf-core/methylseq pipeline

Presenter: Abhinav, Patricia

Links/Resources used:

1. nf-core/methylseq pipeline
   1. Main page: https://nf-co.re/methylseq
   2. Usage: https://nf-co.re/methylseq/2.4.0/usage
      • Example samplesheet: https://github.com/nf-core/methylseq/blob/2.4.0/assets/samplesheet.csv
   3. Parameters: https://nf-co.re/methylseq/2.4.0/parameters
      • Input/Output options: https://nf-co.re/methylseq/2.4.0/parameters#inputoutput-options
      • Alignment options: https://nf-co.re/methylseq/2.4.0/parameters#alignment-options
   4. Output docs: https://nf-co.re/methylseq/2.4.0/output
   5. nf-core/methylseq pipeline options
      • Bismark: https://github.com/FelixKrueger/Bismark
      • BWA-meth: https://github.com/brentp/bwa-meth
      • MethylDackel: https://github.com/dpryan79/methyldackel

2. nf-core/methylseq Github: https://github.com/nf-core/methylseq

   • Test configs: https://github.com/nf-core/methylseq/tree/master/conf

3. Visual Studio Code

   1. Main page: https://code.visualstudio.com/
   2. Documentation: https://code.visualstudio.com/docs