NF-IAP

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).

Installing & Setup

1. Install Nextflow
2. Install Singularity
3. Pull/Clone NF-IAP
4. Get & configure resources
5. Configure nextflow
6. Configure processes

Pull or Clone

Be sure to add the --recursive option to also included the neccessary modules.

git clone git@github.com:UMCUGenetics/NF-IAP.git --recursive

Running the workflow

In this section we'll provide you with a few different ways to run the workflow.

Change the run-template.config to start your analysis

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
}

Starting the full workflow from fastq files

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

Starting the full workflow from from a combination of fastq, bam and gvcf files

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