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Short Description
variant calling with strelka pipeline.
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Strelka pipeline with Nextflow


  1. Install Strelka.
  2. Install nextflow.

     curl -fsSL | bash

    And move it to a location in your $PATH (/usr/local/bin for example here):

     sudo mv nextflow /usr/local/bin


Nextflow seamlessly integrates with GitHub hosted code repositories:

nextflow run iarcbioinfo/strelka-nf --tn_file pairs.txt --bam_path bam_folder/ --ref ref.fasta --strelka path_to_strelka --config strelka_config.ini

Help section

You can print the help manual by providing --help in the execution command line:

nextflow run iarcbioinfo/strelka-nf --help

This shows details about optional and mandatory parameters provided by the user.

pairs.txt format

The pairs.txt file is where you can define pairs of bam to analyse with strelka. It's a tabular file with 2 columns normal and tumor.

normal tumor
normal1.bam tumor2.bam
normal2.bam tumor2.bam
normal3.bam tumor3.bam

Global parameters

--strelka, --config, and --ref are mandatory parameters but can be defined in your nextflow config file (~/.nextflow/config or config in the working directory) and so not set as inputs.

The following is an example of config part defining this:

profiles {

        standard {
                params {
                   ref = '~/Documents/Data/references/hg19.fasta'
                   strelka = '~/bin/strelka/1.0.15/bin/'
                   config = '~/bin/strelka/1.0.15/bin/strelka_config_bwa_default.ini'
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