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.
stringYou 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
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
stringSet 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.
stringOption for QC steps
Skip all QC steps except for MultiQC.
booleanSkip FastQC.
booleanall the trim option are listed below
Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
stringInstructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
stringInstructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
stringInstructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
stringSave the trimmed FastQ files in the results directory.
booleanBy 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.
stringThis 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.
booleanUse 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..
stringRead 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.
booleanNormalization 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.
integer100Reads with an apparent depth of under nx will be presumed to be errors and discarded
integer5save the resulting fastq files from normalization
booleanSpecify which assembler you would like to run, possible alternatives: megahit, rnaspades. default: megahit
stringmegahitPath to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.
stringFilter out contigs shorter than this.
integersave the bam files from mapping
booleanSpecify which ORF caller you would like to run, possible alternatives: prodigal, prokka, transdecoder, default: prodigal.
stringprodigalSpecify a training file for prodigal. By default prodigal will learn from the input sequences
stringSkip EGGNOG functional annotation
booleanSpecify EGGNOG database path
string./eggnogskip kofamscan run
booleanPath to a directory with KOfam files. Will be created if it doesn't exist.
string./kofamIf 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
stringComma-separated list of hmm files which will be searched for among ORFs
stringspecify which pattern hmm files end with
string*.hmmskip eukulele run
booleanSpecify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets
stringmetsEUKulele database.
stringThis 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./eukuleleIf 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
booleanpath to cat database
stringThis 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
booleanThis 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
booleanUse it if you want save the database
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use 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.
string128.GBUse 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.
string240.hUse 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.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
stringAn 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.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleanShow all params when using --help
booleanBy 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.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.