Skip to content
QC samples for PEPPRO pipeline
Branch: master
Clone or download

Latest commit

Fetching latest commit…
Cannot retrieve the latest commit at this time.


Type Name Latest commit message Commit time
Failed to load latest commit information.

Peppro QC PEP

Get source samples using geofetch

geofetch -i sra_accessions.txt -n ppqc

Grab the source sample metadata here:

wget -r .

Get RNA-seq spike-in samples here:

wget[1-9]0pct_RNArc_r2.fastq.gz .

Validate the configuration file with eido like so:

eido -p peppro_paper.yaml -s

Create user-specific environment variables

  • $CODE: this is a path to the parent directory where scripts and code are stored
    • For example:CODE=/scratch/userid/src/
  • $DATA: this is a path to the parent directory where input files are stored
    • For example:DATA=/project/shefflab/data/
  • $PROCESSED: this is a path to the parent directory to where output should be written
    • For example:PROCESSED=/project/shefflab/processed/

Run in looper:

looper run ppqc/peppro_paper.yaml

The peppro_paper.yaml file is the working PEP for these samples. The peppro_paper.csv file is the working annotation file for these samples.

You can’t perform that action at this time.