Run the pipeline¶

Input Requirements¶

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

    nextflow run main.nf \
    -profile <docker/singularity/podman/shifter/charliecloud/conda/institute/test> \
    -entry <QUALITY_ALIGN, FREYJA_ONLY, AQUASCOPE> \
    --input <path/to/samplesheet> \
    --outdir <path/to/out/dir> \
    --fasta </path/to/fasta/> \
    --freyja_barcodes <path_to_barcode_file> \
    --freyja_lineages_meta <path_to_lineage_file> \

Profile (Required)¶

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

Example:

    nextflow run main \
    -profile docker,scicomp_rosalind \
    -entry AQUASCOPE \
    --input <path/to/samplesheet> \
    --outdir <path/to/out/dir>

Entry (Required)¶

Three entry points are available within Aquascope

QUALITY_ALIGN: Runs pipeline beginning from quality control through alignment
FREYJA_ONLY: Runs the pipeline beginning with BAM files through variant calling
AQUASCOPE: Runs both QUALITY_ALIGN followed by FREYJA_ONLY

    nextflow run main.nf \
    -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
    -entry <QUALITY_ALIGN, FREYJA_ONLY, AQUASCOPE> \
    --input <path/to/samplesheet> \
    --outdir <path/to/out/dir> \
    --fasta </path/to/fasta/> \
    --freyja_barcodes <path_to_barcode_file> \
    --freyja_lineages_meta <path_to_lineage_file> \

Samplesheet (Required)¶

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

Example:

    nextflow run main.nf \
    -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
    -entry <QUALITY_ALIGN, FREYJA_ONLY, AQUASCOPE> \
    --input samplesheet.csv \
    --outdir <path/to/out/dir>

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.

NOTES:
- Docker isn't supported on CDC (Rosalind) infrastructure.
- BED file is used for QUALIMAP-BAMQC, GFF in GFF3 format for FREYJA variant calling

Example:

    nextflow run main.nf \
    -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
    -entry <QUALITY_ALIGN, FREYJA_ONLY, AQUASCOPE> \
    --input <path/to/samplesheet> \
    --outdir <path/to/out/dir> \
    --fasta reference.fasta

Freyja Curated Lineages / Barcodes¶

Users can supply saved freyja-curated lineages and barcodes:

    nextflow run main.nf \
    -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
    -entry <QUALITY_ALIGN, FREYJA_ONLY, AQUASCOPE> \
    --input <path/to/samplesheet> \
    --outdir <path/to/out/dir> \
    --freyja_barcodes <path_to_barcode_file> \
    --freyja_lineages_meta <path_to_lineage_file>

Last update: 2024-11-02