/Variant_Calling_Nextflow_pipeline

Pipeline for SNP Calling Created in Nextflow management system for purposesof testing the advantages of managed systems vs native applications in variant calling. The paper created and published one day is titled "NextFlow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data"

Primary LanguageNextflow

You can learn more in our article:

Nextflow vs. plain bash: different approaches to the parallelization of SNP calling from the whole genome sequence data

Three pipelines were used for comparison

  • Native Bash application
  • Single-process Nextflow where all of the pipeline was crammed into single Nextflow process
  • Multi-process Nextflow where each step of the pipeline was seperate Nextflow process (the correct way to design pipeline in managed system such as Nextflow) "Variant_calling_pipeline_nextflow_0.9.nf"

Files used can be found on ncbi database here are coresponding accesion numbers with links: fastq files for individuals: