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Marker alignments in Nextflow

Get Started

  • Install Nextflow

    curl https://get.nextflow.io | bash

Usage

Main parameters:

param value type description
inputPath path to file TSV: sample ID,fastq URL or run ID, [second URL for paired reads]
downloadMethod "sra" / "local"
libraryLayout "single" / "paired"
resultDir path to dir publish directory
refdb path pattern bowtie2 -x parameter
bowtie2Command shell Run bowtie2
alignmentStatsCommand shell samtools stats or other
summarizeAlignmentsCommand shell path to marker_alignments optionally with filter arguments to use
apiKey string ncbi ApiKey

Optional parameters:

param value type description
marker_to_taxon_path path to file summarize_marker_alignments --marker_to_taxon_path parameter

Example

nextflow run VEuPathDB/blastSimilarity -with-trace -c <config_file> -r main

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  • Nextflow 35.4%
  • Perl 30.9%
  • Shell 30.6%
  • Dockerfile 3.1%