...
Then run the nfcore/ampliseq test workflow, which runs on a small test dataset.
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module load java
nextflow run nf-core/ampliseq -r 2.9.0 -profile test,singularity --outdir results
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...
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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
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...
--input "data/samplesheet.tsv" --metadata "data/metadata.tsv" The samplesheet and metadata files you created. Note in this case they must be in a ‘data’ subdirectory, but they can be anywhere you like, which you should then provide the full path for.
...
--outdir results The output directory for results. You can call this whatever you like.
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.
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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
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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
https://nf-co.re/ampliseq/2.9.0/docs/output
Z:\meta_workshop\illumina\results