iarcbioinfo/strelka-nf repository overview

⁠strelka-nf

⁠Strelka pipeline with Nextflow

⁠Dependencies

1. Install Strelka⁠.

2. Install nextflow⁠.

   curl -fsSL get.nextflow.io | bash
   

   Copy

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

   sudo mv nextflow /usr/local/bin
   

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⁠Execution

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.

⁠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'
                }
        }