nf-core/shotgunmetagenomics: parameters

Show all available parameters:

--help: List all available parameters and the default values

Input arguments:

--read_path: Path to a folder containing all input fastq files (this will be recursively searched for *fastq.gz/*fq.gz/*fq/*fastq files)
--reads: Glob pattern to match reads, e.g. '/path/to/reads_*{R1,R2}.fq.gz' (this must be quoted and is in conflict with --read_path)

Output arguments:

--outdir: Pipeline output directory

Decontamination arguments:

--decont_off: Skip trimming and decontamination
--decont_ref_path: Path to the host reference database
--decont_index: BWA index prefix for the host

Profiler configuration:

--profilers: Metagenomics profilers to run. This can be empty, i.e. only run decontamination or a list of profilers delimited with ,, e.g. metaphlan2,humann2,kraken2. By default, the pipeline runs all available profilers.

Kraken2 arguments:

--kraken2_index: Path to the kraken2 database

MetaPhlAn2 arguments:

--metaphlan2_ref_path: Path to the metaphlan2 database
--metaphlan2_index: Bowtie2 index prefix for the marker genes
--metaphlan2_pkl: Python pickle file for marker genes

HUMAnN2 arguments:

--humann2_nucleotide: Path to humann2 chocophlan database
--humann2_protein: Path to humann2 protein database

SRST2 arguments:

--srst2_ref: Fasta file used for srst2

AWSBatch options:

--awsqueue: The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion: The AWS Region for your AWS Batch job to run on