nf-core chipseq

Running the nf-core pipeline

Let’s refer to the usage section of the pipeline’s docs

Using the nf-core launcher

1. Open up the nf-core launch utility

2. Select the rnaseq pipeline, dev for the version and click Launch

3. Fill out the following command-line flags:

   • profile: utd_sysbio
   • input: samplesheet.csv
   • email: <netid>@utdallas.edu
   • read_length: 50
   • genome: hg19

4. Create a file with the nf-params.json file it generates.

nf-params.json

{
  "input": "samplesheet.csv",
  "read_length": 50,
  "outdir": "ming-results",
  "email": "<netid>@utdallas.edu",
  "genome": "hg19"
}

5. We’re going to need to create a samplesheet. Please refer to the usage section of the pipeline’s docs

The data has been predownloaded for you to the class scratch directory /scratch/applied-genomics/ under chipseq/ming/.

samplesheet.csv

sample,fastq_1,fastq_2,antibody,control
WT_YAP1,/scratch/applied-genomics/chipseq/ming/SRR1810900.fastq.gz,,YAP1,WT_INPUT
WT_H3K27ac,/scratch/applied-genomics/chipseq/ming/SRR949140.fastq.gz,,H3K27ac,WT_INPUT
WT_INPUT,/scratch/applied-genomics/chipseq/ming/SRR949142.fastq.gz,,,

Tip

If you can’t get the formatting right for whatever reason there’s a backup samplesheet at /scratch/applied-genomics/chipseq/ming/samplesheet.csv just need to update the input path

6. Start screen which is a screen manager

login$ screen

Useful screen commands

# Start a new screen session:
screen

# Start a new named screen session:
screen -S session_name

# Reattach to an open screen:
screen -r session_name

# Detach from inside a screen:
    Ctrl + A, D

# Kill the current screen session:
    Ctrl + A, K

7. Launch the pipeline

nextflow run nf-core/chipseq -r dev -profile utd_sysbio -params-file nf-params.json

The pipeline should start up, and email you when it’s finished!

While we’re waiting let’s check out the shell script that would’ve ran all of that