04_nf-core_smrnaseq_and_tower-nf.md

SEMINAR 4: Introduction to nf-core/smrnaseq pipeline and Tower

Video link: https://vimeo.com/833512745

Presenter: Chris Hakkart, Patricia

Links/Resources used:

1. Databases

   1. miRBase: https://www.mirbase.org/
   2. MirGeneDB 2.1: https://mirgenedb.org/

2. nf-core/smrnaseq pipeline

   1. Main page: https://nf-co.re/smrnaseq
   2. Usage: https://nf-co.re/smrnaseq/2.2.1/usage
   3. Parameters: https://nf-co.re/smrnaseq/2.2.1/parameters
      • Reference genome/databases: https://nf-co.re/smrnaseq/2.2.1/parameters#reference-genome-options
   4. Sample sheet: https://nf-co.re/smrnaseq/2.2.1/usage#samplesheet-input
   5. miRNA files: https://nf-co.re/smrnaseq/2.2.1/usage#mirna-related-files
   6. Protocols: https://nf-co.re/smrnaseq/2.2.1/usage#protocol
   7. Output docs: https://nf-co.re/smrnaseq/2.2.1/output
   8. nfcore/smrnaseq byte-sized talk https://www.youtube.com/embed/4YLQ2VwpCJE?autoplay=1
   9. nfcore/smrnaseq Github: https://github.com/nf-core/smrnaseq
      • Test configs: https://github.com/nf-core/smrnaseq/tree/master/conf

3. Nextflow Tower: https://cloud.tower.nf/

   1. Tower documentation: https://help.tower.nf/23.1/
   2. Nextflow training; tower: https://training.nextflow.io/basic_training/tower/

4. Nextflow config files: https://nextflow.io/docs/latest/config.html