Nextflow Illumina Analysis Pipeline. Includes pre/post-mapping QC, BWA mapping & GATK germline calling and variant annotation. The workflow is able to start from multiple entry points (e.g. fastq, bam, gvcf or vcf).
- Install Nextflow
- Install Singularity
- Pull/Clone NF-IAP
- Get & configure resources
- Configure nextflow
- Configure processes
Be sure to add the --recursive option to also included the neccessary modules.
git clone [email protected]:UMCUGenetics/NF-IAP.git --recursive
In this section we'll provide you with a few different ways to run the workflow.
Always keep these lines in your run.config file:
includeConfig '/path/to/config/nextflow.config'
includeConfig '/path/to/config/process.config'
includeConfig '/path/to/config/resources.config'
All of the parameters in the params section can also be supplied on the commandline or can be pre-filled in the run.config file.
params {
fastq_path = ''
bam_path = ''
vcf_path = ''
gvcf_path = ''
out_dir = ''
genome = 'GRCh37'
premapQC = true
postmapQC = true
germlineCalling = true
variantFiltration = true
variantAnnotation = true
}
Create the run.config file to look like this:
params {
fastq_path = '/path/to/fastqfiles/'
bam_path = ''
vcf_path = ''
gvcf_path = ''
out_dir = ''
genome = 'GRCh37'
premapQC = true
postmapQC = true
germlineCalling = true
variantFiltration = true
variantAnnotation = true
}
Run the workflow on sge :
nextflow run nf-iap.nf -c run.config --out_dir /processed_data/runX/ -profile sge -resume
Create the run.config file to look like this:
params {
fastq_path = '/path/to/fastqfiles/'
bam_path = '/path/to/bamfiles/'
vcf_path = ''
gvcf_path = '/path/to/gvcffiles/'
out_dir = ''
genome = 'GRCh37'
premapQC = true
postmapQC = true
germlineCalling = true
variantFiltration = true
variantAnnotation = true
}
Run the workflow on slurm :
nextflow run nf-iap.nf -c run.config --out_dir /processed_data/runX/ -profile slurm -resume
Starting only the variant annotation on one or more vcf files (can't be combined with fastq's,bam's or gvcf's).
params {
fastq_path = ''
bam_path = ''
vcf_path = '/path/to/vcffiles/'
gvcf_path = ''
out_dir = ''
genome = 'GRCh37'
premapQC = false
postmapQC = false
germlineCalling = false
variantFiltration = false
variantAnnotation = true
}
Run the workflow on slurm :
nextflow run nf-iap.nf -c run.config --out_dir /processed_data/runX/ -profile slurm -resume
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