Run the pipeline¶

Input Requirements¶

To run the pipeline, the following inputs may be given at run-time: - profile (required) - samplesheet - references file (optional) - Freyja-specific files (optional)

Profile (Required)¶

Select from any of the profiles: - docker - singularity - podman - shifter - charliecloud - conda - instutitute_specific_profiles

```
nextflow run main.nf \
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
--input samplesheet.csv \
--outdir results
```

These profiles can be combined together

```
nextflow run main \
-profile docker,rosalind_uge \
--input samplesheet.csv \
--outdir results
```

Samplesheet (Required)¶

Refer to the Preparing Files documentaiton for specific samplesheet-related instructions.

References (Optional)¶

Fasta, bed and gff parameters are defaulted to references in the assets folder of the pipeline. To change, the --fasta, --gff and --gff3 are available as input parameters.

• Bed file is used for QUALIMAP-BAMQC, GFF in GFF3 format for FREYJA variant calling

• Docker isn't supported on CDC (Rosalind) infrastructure.

  nextflow run main.nf \
  -profile <docker/singularity> \
  --input samplesheet.csv \
  --outdir results \
  --fasta /path/to/fasta/
  

Freyja Curated Lineages / Barcodes¶

Users can supply saved freyja-curated lineages and barcodes:

nextflow run main.nf \ -profile <docker/singularity> \ --input samplesheet.csv \ --freyja_barcodes <path_to_barcode_file> \ --freyja_lineages_meta <path_to_lineage_file> \ --outdir results