Marker alignments in Nextflow

Installation

This workflow is not containerised, but the dependencies are quite minimal:

• bowtie2
• Marker alignments package and its tool marker_alignments.

Additionally, samtools stats is the default and recommended for alignment stats.

By default, bowtie2, marker_alignments and samtools are assumed to be on $PATH but you can provide a path to an executable in the pipeline config.

If you want to use --downloadMethod wget you also need wget. If you want to use --downloadMethod sra you need the SRA EUtils, with prefetch and fastq-dump on $PATH.

--unpackMethod bz2 requires bzip2 on $PATH.

You also need a bowtie2 reference database of taxonomic markers, like ChocoPhlAn or EukDetect.

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	"wget" / "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

Optional parameters:

param	value type	description
marker_to_taxon_path	path to file	summarize_marker_alignments --marker_to_taxon_path parameter
unpackMethod	"bz2"	for FTP .tar.bz2 content

Example

I run it like that:

run.sh

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
REF_PATH="~/eukprot"

nextflow pull wbazant/marker-alignments-nextflow -r main

nextflow run wbazant/marker-alignments-nextflow -r main \
  --inputPath $DIR/in.tsv  \
  --resultDir $DIR/results \
  --downloadMethod wget \
  --unpackMethod bz2 \
  --libraryLayout paired \
  --refdb ${REF_PATH}/ncbi_eukprot_met_arch_markers.fna \
  --marker_to_taxon_path ${REF_PATH}/busco_taxid_link.txt  \
  -c $DIR/cluster.conf \
  -with-trace -resume | tee $DIR/tee.out

cluster.conf

process {
  executor = 'lsf'
  maxForks = 60
  
  withLabel: 'download' {
    maxForks = 5
    maxRetries = 3
  }
  withLabel: 'align' {
    errorStrategy = 'finish'
  }
}

in.tsv

SRS011061       https://downloads.hmpdacc.org/dacc/hhs/genome/microbiome/wgs/analysis/hmwgsqc/v1/SRS011061.tar.bz2
SRS011086       https://downloads.hmpdacc.org/dacc/hhs/genome/microbiome/wgs/analysis/hmwgsqc/v1/SRS011086.tar.bz2