...
| Code Block |
|---|
wget https://www.mirbase.org/download/CURRENT/mature.fa gzip -c mature.fa.gz |
Run a test
Prior Before running the pipeline with real data, run the following test:
| Code Block |
|---|
nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.21.10 |
To submit the above command to the HPC cluster prepare the following script:
| Code Block |
|---|
#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR
#load java and set up memory settings to run nextflow
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.1.0 |
Submitting the job
Once you have created the folder for the run, the samplesheet.csv file, nextflow.config, and launch.pbs, you are ready to submit.
Submit the run with this command
| Code Block |
|---|
qsub launch.pbs |
Monitoring the Run
You can use the command
| Code Block |
|---|
qstat -u $USER |
Alternatively, use the command
| Code Block |
|---|
qjobs |
to check on the jobs, you are running. Nextflow will launch additional jobs during the run.
You can also check the .nextflow.log file for details on what is going on.
Preparing a sample metadata file
Now let’s prepare a samplesheet.csv file that specifies the name of your samples and the location of the raw FASTQ files
| Code Block |
|---|
#!/bin/bash -l #PBS -N nfsmrnaseq #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=12:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR #User defined variables ########################################################## DIR='/path/to/raw/FASTQ/files' INDEX='samplesheet.csv' ########################################################## #load python module module load python/3.10.8-gcccore-12.2.0 #fetch the script to create the sample metadata table wget -L https://raw.githubusercontent.com/nf-core/rnaseq/master/bin/fastq_dir_to_samplesheet.py chmod +x fastq_dir_to_samplesheet.py #generate initial sample metadata file ./fastq_dir_to_samplesheet.py $DIR index.csv \ --strandedness auto \ --read1_extension .fastq.gz #format index file cat index.csv | awk -F "," '{print $1 "," $2}' > ${INDEX} #Remove intermediate files: rm index.csv fastq_dir_to_samplesheet.py |