/diagnostic-check-nf

Primary LanguageNextflow

manta-strelka-vc

A Nextflow pipeline to run manta and strelka variant callers.

The pipeline is meant to process a pair of samples per patient: normal and tumour. Therefore, generating somatic variant calling.

Requirements

The only requirements are to have Nextflow and docker installed in the system.

Usage

This pipeline requires the following files:

  • Input CSV file describing the patient ID, sample name and file paths to the input bam and bai files. The following columns are required:
    • patient_id: id of the patient. The file should contain two rows per patient, one for the Normal sample and the other for the tumour sample.
    • sample_id: id of the patient sample.
    • tumor_normal: an uppercase "N" or "T" to specify Normal or Tumour sample.
    • bam: path, ftp or s3 bucket of the bam mapping file.
    • bai: path, ftp or s3 bucket of the bai index file.

An example of input CSV file could be found at testdata/test_input.csv:

patient_id,sample_id,tumor_normal,bam,bai
pb,pb_normal,N,testdata/pb_normal.bam,testdata/pb_normal.bam.bai
pb,pb_tumor,T,testdata/pb_tumor.bam,testdata/pb_tumor.bam.bai
  • A genome fasta file corresponding to the assembly used while mapping the input files.
  • A genome fasta fai index file of the genome fasta provided.

Local tests

Clone the repo:

git clone https://github.com/lifebit-ai/manta-strelka-vc.git
cd manta-strelka-vc

Then, run the pipeline:

nextflow main.nf --config conf/test.config

CloudOS tests

Use the --config conf/test.config parameter and open an instance with at least 2 CPUs and 3GB of RAM.