Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
106 lines (77 sloc) 2.72 KB

Usage

Display Help Message

The help parameter displays the available options and commands.

$ nextflow run main_amr_plus_plus_v2.nf --help

File Inputs

Set custom sequence data

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

$ nextflow run main_amr_plus_plus_v2.nf --reads "data/raw/*_R{1,2}.fastq"

Set host genome

The host parameter accepts a fasta formatted host genome.

$ nextflow run main_amr_plus_plus_v2.nf --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 main_amr_plus_plus_v2.nf --host "data/host/chr21.fasta.gz" --index "data/index/*"

Set resistance database

The amr parameter accepts a fasta formatted resistance database.

$ nextflow run main_amr_plus_plus_v2.nf --amr "data/amr/megares_database_v1.02.fasta"

Set annotation database

The annotation parameter accepts a csv formatted annotation database.

$ nextflow run main_amr_plus_plus_v2.nf --annotation "data/amr/megares_annotations_v1.02.csv"

Set adapter file

The adapters parameter accepts a fasta formatted adapter file.

$ nextflow run main_amr_plus_plus_v2.nf --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 main_amr_plus_plus_v2.nf --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 main_amr_plus_plus_v2.nf --output "test/" -work "work_dir/" -resume

Trimming Options

Set custom trimming parameters

$ nextflow run main_amr_plus_plus_v2.nf \
    --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 main_amr_plus_plus_v2.nf \
    --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 main_amr_plus_plus_v2.nf --threads 8
You can’t perform that action at this time.