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
-
Select the
rnaseq
pipeline,dev
for the version and click Launch -
Fill out the following command-line flags:
- profile:
utd_sysbio
- input:
samplesheet.csv
- email:
<netid>@utdallas.edu
- read_length: 50
- genome:
hg19
- profile:
-
Create a file with the
nf-params.json
file it generates.
{ "input": "samplesheet.csv", "read_length": 50, "outdir": "ming-results", "email": "<netid>@utdallas.edu", "genome": "hg19"}
- 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/
.
sample,fastq_1,fastq_2,antibody,controlWT_YAP1,/scratch/applied-genomics/chipseq/ming/SRR1810900.fastq.gz,,YAP1,WT_INPUTWT_H3K27ac,/scratch/applied-genomics/chipseq/ming/SRR949140.fastq.gz,,H3K27ac,WT_INPUTWT_INPUT,/scratch/applied-genomics/chipseq/ming/SRR949142.fastq.gz,,,
- 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
- 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