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Display Help Message

The help parameter displays the available options and commands.

$ nextflow run --help

File Inputs

Set custom sequence data

The reads parameter accepts sequence files in standard fastq and gz format.

$ nextflow run --reads "data/raw/*_R{1,2}.fastq"

Set host genome

The host parameter accepts a fasta formatted host genome.

$ nextflow run --host "data/host/chr21.fasta.gz"

Set host index

The index parameter allows you to upload pre-built host indexes produced by BWA.

$ nextflow run --host "data/host/chr21.fasta.gz" --index "data/index/*"

Set resistance database

The amr parameter accepts a fasta formatted resistance database.

$ nextflow run --amr "data/amr/megares_database_v1.02.fasta"

Set annotation database

The annotation parameter accepts a csv formatted annotation database.

$ nextflow run --annotation "data/amr/megares_annotations_v1.02.csv"

Set adapter file

The adapters parameter accepts a fasta formatted adapter file.

$ nextflow run --adapters "data/adapters/adapters.fa"

File Outputs

Set output and work directories

The output parameter writes the results to the specified directory. As a nextflow variable, the work parameter only requires one dash and determines where the temporary files will be directed. Upon completing the run, you can delete the temporary file directory.

$ nextflow run --output "test/" -work "work_dir/"

Resume a pipeline run

If the pipeline run is cancelled or stopped for whatever reason, using the same command with the addition of the -resume flag will attempt to pick up where the pipeline stopped.

$ nextflow run --output "test/" -work "work_dir/" -resume

Trimming Options

Set custom trimming parameters

$ nextflow run \
    --reads "data/raw/*_R{1,2}.fastq" \
    --leading 3 \
    --trailing 3 \
    --minlen 36 \
    --slidingwindow 4 \
    --adapters "data/adapters/nextera.fa"
    --output "test/"

Algorithm Options

Set custom algorithm options

$ nextflow run \
    --reads "data/raw/*_R{1,2}.fastq" \
    --threshold 80 \
    --min 1 \
    --max 100 \
    --samples 5 \
    --skip 5 \
    --output "test/"

Set number of threads to use for each process

$ nextflow run --threads 8
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