Marker alignments in Nextflow

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

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

Name		Name	Last commit message	Last commit date
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bin		bin
data		data
modules		modules
Dockerfile		Dockerfile
Jenkinsfile		Jenkinsfile
LICENSE		LICENSE
README.md		README.md
main.nf		main.nf
nextflow.config		nextflow.config