...

Then run the nfcore/ampliseq test workflow, which runs on a small test dataset.

module load java
nextflow run nf-core/ampliseq -r 2.9.0 -profile test,singularity --outdir results

...

The workflow takes approximately 40 minutes to complete.

Running again, with metadata

In the previous run to save time we didn’t include the dummy metadata. You can run it in the background now with the metadata option included, to see how it runs.

cd $HOME/meta_workshop/illumina
module load java
nextflow run nf-core/ampliseq -r 2.9.0 -profile singularity --single_end --ignore_failed_trimming --input "data/samplesheet.tsv" --metadata "data/metadata.tsv" --FW_primer "GGATTAGATACCCBRGTAGTC" --RV_primer "TCACGRCACGAGCTGACGAC" --outdir results_with_metadata

Additional parameters:

--metadata "data/metadata.tsv" Include the metadata file

--outdir results_with_metadata Output results to a new directory, called results_with_metadata

Interpreting ampliseq results

...