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.
string
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
boolean
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
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.
string
Option for QC steps
Skip all QC steps except for MultiQC.
boolean
Skip FastQC.
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).
string
Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
string
Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
string
Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
string
Save the trimmed FastQ files in the results directory.
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.
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.
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..
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.
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.
integer
100
Reads with an apparent depth of under nx will be presumed to be errors and discarded
integer
5
save the resulting fastq files from normalization
boolean
Specify which assembler you would like to run, possible alternatives: megahit, rnaspades. default: megahit
string
megahit
Path to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.
string
Filter out contigs shorter than this.
integer
save the bam files from mapping
boolean
Specify which ORF caller you would like to run, possible alternatives: prodigal, prokka, transdecoder, default: prodigal.
string
prodigal
Specify a training file for prodigal. By default prodigal will learn from the input sequences
string
Skip EGGNOG functional annotation
boolean
Specify EGGNOG database path
string
./eggnog
skip kofamscan run
boolean
Path to a directory with KOfam files. Will be created if it doesn't exist.
string
./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
string
Comma-separated list of hmm files which will be searched for among ORFs
string
specify which pattern hmm files end with
string
*.hmm
skip eukulele run
boolean
Specify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets
string
mets
EUKulele database.
string
This option allows the user to specify which database (or set of databases, separated by comma) 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.
string
./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).
run cat taxonomy annotation
boolean
path to cat database
string
This parameter is mutually exclusive with ´cat_db_generate´. You need to provide a version of CAT database that has the same DIAMOND version of the module (DIAMOND 2.0.8) otherwise you might encounter issues of incompatibility and the module will fail. We recommend to always use the database provided by CAT website: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/
It will run a CAT command that will download the database
boolean
This parameter is mutual exclusive with cat_db
. when activated, cat_db_generate
will run a module in order to download and prepare a CAT database.
Use it if you want assign official taxonomy
boolean
Use it if you want save the database
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
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.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
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.
string
128.GB
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.
string
240.h
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.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
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.
string
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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
Show all params when using --help
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.
boolean
By default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
boolean
Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.