Define where the pipeline should find input data and save output data.

Path to comma-separated file containing information about the samples in the experiment.

required
type: string
pattern: ^\S+\.csv$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.

activate when using single end reads input

type: boolean

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string
default: ./results

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Option for QC steps

Skip all QC steps except for MultiQC.

type: boolean

Skip FastQC.

type: boolean

all the trim option are listed below

Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).

type: string

Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).

type: string

Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.

type: string

Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.

type: string

Save the trimmed FastQ files in the results directory.

type: boolean

By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.

Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.

type: string

This enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.

Skip the adapter trimming step.

type: boolean

Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.

Fasta file with sequences to filter away before running assembly etc..

type: string

Read sequences matching this file will be filtered out from samples with BBDuk before mapping. If no file is specified, BBDuk will not be run.

Use these option if you need to normalize the reads before the assembly

Perform normalization to reduce sequencing depth.

type: boolean

Normalization is performed following the example in https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/

Reduce the number of reads for assembly average coverage of this number.

type: integer
default: 100

Reads with an apparent depth of under nx will be presumed to be errors and discarded

type: integer
default: 5

save the resulting fastq files from normalization

type: boolean

Specify which assembler you would like to run, possible alternatives: megahit, spades. default: megahit

type: string

Path to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.

type: string

Filter out contigs shorter than this.

type: integer

Select which type of assembly you want to make. Default: rna

type: string

This option allows you to run an assembly for a different scope. For instance, with '--spades_flavor rna' you will get an assembly for prokaryotic metatrancriptomes, --spades_flavor rnaviral' for viral metatranscriptomes or --spades_flavor metaviralfor viral metagenomes. The argument to the parameter will be passed as a parameter to Spades; e.g.--spades_flavor rnawill be passed as--rna` to Spades.

Save the formatted spades fasta file

type: boolean

Save the bam files from mapping

type: boolean

Save the output from samtools

type: boolean

Minimum identity needed to assign read to a contig

type: number
default: 0.9

Path to a protein fasta file

type: string

Path to a gff file

type: string

Specify which ORF caller you would like to run, possible alternatives: prodigal, prokka, transdecoder, default: prodigal.

type: string

Specify a training file for prodigal. By default prodigal will learn from the input sequences

type: string

Size of individual files annotated by Prokka in one batch.

hidden
type: string
default: 10 MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Prokka usually fails on very large input files. This parameter controls the size of smaller batches for which Prokka will be called. Should be a string in the format integer-unit e.g. --prokka_batchsize '8.MB'

Skip EGGNOG functional annotation

type: boolean

Specify EGGNOG database path

type: string
default: eggnog

This parameter specifies where you have an EGGNOG database, or, where it will be created using the --create_eggnog_db parameter. The directory must exist.

skip kofamscan run

type: boolean

Path to a directory with KOfam files. Will be created if it doesn't exist.

type: string
default: ./kofam/

If a ko_list file and/or profiles does not exist, they will be downloaded.

Directory with hmm files which will be searched for among ORFs

type: string
pattern: ^\S+

Comma-separated list of hmm files which will be searched for among ORFs

type: string
pattern: \S+hmm(\.gz)?

specify which pattern hmm files end with

type: string
default: *.hmm

skip eukulele run

type: boolean

Specify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets

type: string

EUKulele database.

type: string

This option allows the user to specify which database to use with EUKulele. Databases that are provided with EUKulele will be downloaded if not already present inside the database directory (see --eukulele_dbpath). Possible alternatives: phylodb, mmetsp, marmmetsp, eukprot. NB: you can't use this option with a custom database as eukulele will not recognize the name and it will start to download phylodb by default. If you want to use a custom database, please skip this option and specify only --eukulele_dbpath.

EUKulele database folder.

type: string
default: ./eukulele/

If this parameter is set, EUKulele will look for a database to use in this folder. If --eukulele_db also is set, the specified database will be searched for in this directory and if it is not present it will be downloaded. If a custom database (see EUKulele documentation) should be used, EUKulele will assume that it is present in this folder - N.B. only works with one custom database (if using a custom database, point to a directory that only contains that database).

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean

Show all params when using --help

hidden
type: boolean

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.

Valitadion S3 path

type: string

Validation dupliacate check

type: string

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/