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Usage

Usage

Display Help Message

The help parameter displays the available options and commands. 

nextflow run main_AMR++.nf --help

Parameter selection

AMR++ comes with a default selection of parameters to perform a demonstration using example data provided in the "data/" directory. The example command below uses two types of parameters. 

nextflow run main_AMR++.nf -profile singularity --pipeline demo

The -profile parameter only has a single dash (-), meaning it corresponds to a nextflow-speific parameter and the --pipeline. Examples of parameters with one dash include -profile, -resume, and -config. Further details on using the profile parameter, which determines how AMR++ runs on a computing cluster, can be found in the configuration document. Below, we'll see how to change the pipeline-specific parameters which are denoted using two dashes (--), such as --pipeline and --reads.

The AMR++ pipeline pulls information from various sources to determine the correct parameters for running the pipeline. AMR++ is written in nextflow and this allows for us to change how the pipeline runs in a variety of ways. This is the order in which nextflow will prioritize parameters it receives.

  1. Parameters specified on the command line (--something value)

  2. Parameters provided using the -params-file option (params.config by default)

  3. Config file specified using the -c my_config option (e.g. config/local.config)

  4. The config file named nextflow.config in the current directory

  5. The config file named nextflow.config in the workflow project directory

  6. The config file $HOME/.nextflow/config

  7. Values defined within the pipeline script itself (e.g. main_AMR++.nf)

File Inputs

Set custom sequence data

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

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

Set host genome

The host parameter accepts a fasta formatted host genome. 

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

Set MEGARes resistance database

The amr parameter accepts a fasta formatted resistance database. AMR++ is made to work with MEGARes databases and has to have the corresponding --annotation file in csv format.

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

Set MEGARes annotation database

The annotation parameter accepts a csv formatted annotation database. Note, this must match the resistance database that was used above for the ResistomeAnalyzer and RarefactionAnalyzer steps to work correctly. 

$ nextflow run main_AMR++.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++.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++.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. This "work" directory can take a lot of storage space and we recommend deleting it after completion of the pipeline.

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

Trimming Options

Set custom trimming parameters for trimmomatic

$ nextflow run main_AMR++.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 ResistomeAnalyzer algorithm options

$ nextflow run main_AMR++.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 (when possible)

$ nextflow run main_AMR++.nf --threads 8

Run AMR++ with SLURM

Adding the -bg flag submits AMR++ to the SLURM queue and when combined with a "slurm" profile, jobs will be submitted for each individual process in the pipeline.

nextflow run main_AMR++.nf -profile local_slurm --snp Y -bg > bg-log.out