Usage
Warning
This documentation is for AMR++ version 2.0. Click here for the latest docs.
Display Help Message
The help
parameter displays the available options and commands.
$ nextflow run main_AmrPlusPlus_v2.nf --help
File Inputs
Set custom sequence data
The reads
parameter accepts sequence files in standard fastq and gz format.
$ nextflow run main_AmrPlusPlus_v2.nf --reads "data/raw/*_R{1,2}.fastq"
Set host genome
The host
parameter accepts a fasta formatted host genome.
$ nextflow run main_AmrPlusPlus_v2.nf --host "data/host/chr21.fasta.gz"
Set host index
The host_index
parameter allows you to upload pre-built host indexes produced by BWA.
$ nextflow run main_AmrPlusPlus_v2.nf --host "data/host/chr21.fasta.gz" --host_index "data/index/*"
Set resistance database
The amr
parameter accepts a fasta formatted resistance database.
$ nextflow run main_AmrPlusPlus_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_AmrPlusPlus_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_AmrPlusPlus_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_AmrPlusPlus_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_AmrPlusPlus_v2.nf --output "test/" -work "work_dir/" -resume
Trimming Options
Set custom trimming parameters
$ nextflow run main_AmrPlusPlus_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_AmrPlusPlus_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_AmrPlusPlus_v2.nf --threads 8