Usage¶

Samplesheet¶

advena takes a CSV samplesheet as input, with one genome per row:

sample,genbank
GCF_000009045,/data/GCF_000009045.gbff
GCF_003176835,/data/GCF_003176835.gbff

Column	Description
`sample`	Unique sample identifier used in all output filenames
`genbank`	Path to a GenBank file (`.gb` or `.gbff`)

An example samplesheet is provided in assets/samplesheet.csv.

Basic usage¶

nextflow run exterex/advena \
    --input samplesheet.csv \
    --outdir results \
    -profile docker

Container engine profiles¶

Combine a container engine profile with an optional execution profile:

# Docker (local)
-profile docker

# Singularity on an HPC cluster
-profile singularity,hpc

# SLURM cluster with Singularity
-profile singularity,slurm

# Conda (local)
-profile conda

# Test dataset with Docker
-profile test,docker

Specifying the ICEscreen installation¶

advena reads the ICEscreen Python scripts and databases at runtime. There are three ways to provide the paths:

Environment variable (recommended): Set ICESCREEN_ROOT before running the pipeline.

export ICESCREEN_ROOT=/opt/icescreen
nextflow run exterex/advena --input samplesheet.csv --outdir results -profile docker

Pipeline parameter: Pass --icescreen_root directly.

nextflow run exterex/advena \
  --input samplesheet.csv \
  --outdir results \
  --icescreen_root /opt/icescreen \
  -profile docker

Override database path: Use --icescreen_db to override database path.

nextflow run exterex/advena \
  --input samplesheet.csv \
  --outdir results \
  --icescreen_db /data/icescreen_databases \
  -profile docker

Resuming a run¶

Nextflow caches completed tasks. If a run is interrupted, resume from where it left off:

nextflow run exterex/advena \
    --input samplesheet.csv \
    --outdir results \
    -profile docker \
    -resume

Adjusting BLAST parameters¶

The BLASTP search sensitivity can be tuned with --blastp_evalue and --blastp_max_target_seqs:

nextflow run exterex/advena \
    --input samplesheet.csv \
    --outdir results \
    --blastp_evalue 1e-5 \
    --blastp_max_target_seqs 5 \
    -profile docker

Adjusting ME detection parameters¶

Mobile element segmentation thresholds can be adjusted for non-standard genomes:

nextflow run exterex/advena \
    --input samplesheet.csv \
    --outdir results \
    --min_cds_between_segments 50 \
    --max_cds_for_ime_size 20 \
    -profile docker