Exercise 2: Run nf-core/sarek using a family trio data (HapMap; Genome in a Bottle)
Public data
Family ID: 1463
Family information: family lineage from Utah of four grandparents, two parents, and 11 children (17 family members)
Genomics consortia: Genome in a Bottle, 1000 Genomes Project, International HapMap Project, Centre d'Etude du Polymorphisme Humain (CEPH)
...
The pipeline requires preparing at least 2 files:
Metadata file (samplesheet.csv) thatspecifies the following information:
| Code Block |
|---|
patient,sample,lane,fastq_1,fastq_2 ID1,S1,L002,/full/path/to/ID1_S1_L002_R1_001.fastq.gz,/full/path/to/ID1_S1_L002_R2_001.fastq.gz |
PBS Pro script (launch_nf-core_sarek_trio.pbs) with instructions to run the pipeline (see below)
STEP1: Create the metadata file (samplesheet.csv):
List FASTQ files in the data folder directory of the family trio:
...
| Code Block |
|---|
cp $HOME/workshop/sarek/scripts/create_samplesheet_nf-core_sarek.py $HOME/workshop/sarek/run2_trio cd $HOME/workshop/sarek/run2_trio |
Note: you could replace ‘$HOME/workshop/sarek/data’ with “.” A dot indicates ‘current directory’ and will copy the file to the directory where you are currently located
Check help option on how to run the script:
...
| Code Block |
|---|
python create_samplesheet_nf-core_sarek.py --dir /work/training/sarek/data/WES/trio \
--read1_extension R1.fastq.gz \
--read2_extension R2.fastq.gz \
--out samplesheet.csv |
Alternatively copy the samplesheet.csv file:
| Code Block |
|---|
cp /work/training/sarek/data/WES/trio/samplesheet.csv . |
Check the newly created samplesheet.csv file:
| Code Block |
|---|
ls -l cat samplesheet.cvscsv |
patient,sample,lane,fastq_1,fastq_2 SRR14724455,NA12892a,L001,/sarek/data/WES/trio/SRR14724455_NA12892a_L001_R1.fastq.gz,/sarek/data/WES/trio/SRR14724455_NA12892a_L001_R2.fastq.gz SRR14724456,NA12891a,L001,/sarek/data/WES/trio/SRR14724456_NA12891a_L001_R1.fastq.gz,/sarek/data/WES/trio/SRR14724456_NA12891a_L001_R2.fastq.gz SRR14724463,NA12878a,L001,/sarek/data/WES/trio/SRR14724463_NA12878a_L001_R1.fastq.gz,/sarek/data/WES/trio/SRR14724463_NA12878a_L001_R2.fastq.gz SRR14724474,NA12892b,L001,/sarek/data/WES/trio/SRR14724474_NA12892b_L001_R1.fastq.gz,/sarek/data/WES/trio/SRR14724474_NA12892b_L001_R2.fastq.gz SRR14724475,NA12891b,L001,/sarek/data/WES/trio/SRR14724475_NA12891b_L001_R1.fastq.gz,/sarek/data/WES/trio/SRR14724475_NA12891b_L001_R2.fastq.gz SRR14724483,NA12878b,L001,/sarek/data/WES/trio/SRR14724483_NA12878b_L001_R1.fastq.gz,/sarek/data/WES/trio/SRR14724483_NA12878b_L001_R2.fastq.gz |
|---|
STEP 2: running the nf-core/sarek pipeline (launch_nf-core_sarek_trio.pbs)
Copy and paste the code below to the terminal:
| Code Block |
|---|
cp $HOME/workshop/sarek/scripts/launch_nf-core_sarek_trio.pbs $HOME/workshop/sarek/run2_trio cd $HOME/workshop/sarek/run2_trio |
Line 1: copy the launch_nf-core_sarek_trio.pbs submission script to the working directory
Line 2: move to the working directory
View the content of the launch_nf-core_sarek_trio.pbs script:
...
#!/bin/bash -l #PBS -N nfsarek_run2_trio #PBS -l walltime=48:00:00 #PBS -l select=1:ncpus=1:mem=5gb cd $PBS_O_WORKDIR NXF_OPTS='-Xms1g -Xmx4g' module load java #specify the nextflow version to use to run the workflow export NXF_VER=23.10.1 #run the sarek pipeline nextflow run nf-core/sarek \ -r 3.3.2 \ -profile singularity \ --genome GATK.GRCh38 \ --input samplesheet.csv \ --wes \ --outdir ./results \ --step mapping \ --tools haplotypecaller,snpeff,vep \ --snpeff_cache /work/training/sarek/NXF_SINGULARITY_CACHEDIR/snpeff_cache \ --vep_cache /work/training/sarek/NXF_SINGULARITY_CACHEDIR/vep_cache \ -resume |
|---|
The above script will screen for germline (inherited) mutations using GATK’s haplotypecaller and then annotate the identified variants using snpeff and VEP.
Version 3.3.2 allows running the pipeline to do quality assessment only, without any alignment, read counting, or trimming.
The pipeline enables use to start at distinct stages, we are commencing from the start “--step mapping”
Pipeline steps:
mapping
markduplicates
prepare_recalibration
recalibrate
variant_calling
annotation
See more information on the input requirements for each step https://nf-co.re/sarek/3.3.2/docs/usage
...
Once the pipeline has finished running - Assess the results as follows:
NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.
To browse the working folder in the HPC type in the file finder:
...
During execution of the workflow two output folders are generated:
work - where all intermediate results and tasks are run
results - where all final results for all stages of the pipeline are copied
...