nf-core pipeline for taxonomy profiling

The nf-core/taxpfoiler (https://nf-co.re/taxprofiler) will be used in this training. It consists of serveral best practice profilers: e.g., mOTUs and metaPhlAn.

  • Download reference databases

cd /mnt

wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/mg_databases/db_mOTU_v3.1.0.tar.gz
tar zvxf db_mOTU_v3.1.0.tar.gz

mkdir -p output_taxprofiler

  • Set the database path with vi databases.csv

tool,db_name,db_params,db_path
motus,db_mOTU,,/mnt/db_mOTU

  • Prepare sample sheet file with vi samples.csv

sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
s1,run1,ILLUMINA,/mnt/WGS-data/read1.fq.gz,/mnt/WGS-data/read2.fq.gz,

  • Run the pipeline

nextflow run nf-core/taxprofiler \
  --input samples.csv \
  --databases databases.csv \
  --outdir output_taxprofiler \
  -profile singularity \
  --run_motus \
  --motus_use_relative_abundance

After the pipeline finished, we can will have all results in the output_taxprofiler directory.