Peppro QC PEP
Get source samples using geofetch
geofetch -i sra_accessions.txt -n ppqc
Grab the source sample metadata here:
wget -r http://big.databio.org/peppro/sra_meta/ppqc/ .
Get RNA-seq spike-in samples here:
wget http://big.databio.org/peppro/fastq/K562_[1-9]0pct_RNArc_r2.fastq.gz .
Validate the configuration file with eido like so:
eido -p peppro_paper.yaml -s http://schema.databio.org/pipelines/ProseqPEP.yaml
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/
- For example:
$DATA: this is a path to the parent directory where input files are stored- For example:
DATA=/project/shefflab/data/
- For example:
$PROCESSED: this is a path to the parent directory to where output should be written- For example:
PROCESSED=/project/shefflab/processed/
- For example:
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.