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Version: Summer 22

nf-core

nf-core Intro​

A community effort to collect a curated set of analysis pipelines built using Nextflow.

We have the genomics core, imaging core, etc. core facilities, and nf-core!

Enough talk, let's run it!

Testing a pipeline​

nf-core installation docs

  1. Move into your chipseq repo
  2. Install Nextflow
curl -fsSL get.nextflow.io | bash
mv nextflow ~/bin
  1. Activate singularity
ml load singularity
  1. Run
nextflow run nf-core/chipseq -profile test,utd_sysbio -r dev --outdir test-run
  1. Update your .gitignore
.nextflow*
work/
data/
results/

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 chipseq 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"
}
  1. 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

  1. Start screen which is a screen manager
login$ screen
info

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
  1. 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

Download the Multiqc Report​

  1. Open up the file explorer and navigate to results/multiqc/multiqc_report.html and right-click the html file and select Download.
  2. Now that the multiqc report is on your local computer open it up in a web browser. Preferably next to the pipeline's output docs.