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. See usage docs.

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

required
type: string

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

Save all intermediate files (e.g. fastq, bams) to output directory

type: boolean

Options for processing reads with unique molecular identifiers

Enable UMI-based read deduplication.

type: boolean

UMI pattern to use. Can be either 'string' (default) or 'regex'.

type: string
default: string

More details can be found in the UMI-tools documentation.

UMI grouping method

type: string
default: dir

Available options are dir, cc, adj

Skip the UMI extraction from the reads before deduplication. Please note, if this parameter is set to false, the reads will be deduplicated solely on insert sequence. UMIs might be extracted after deduplication depending on the set umitools_bc_pattern nevertheless if with_umi is set to True.

type: boolean
default: true

The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.

type: string

More details can be found in the UMI-tools documentation.

After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.

type: integer

If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.

type: boolean

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Boolean whether MirGeneDB should be used instead of miRBase

type: boolean

This allows you to use MirGeneDB instead of miRBase as the database.
Note that you will need to set the additional flags --mirgenedb_species, --mirgenedb_gff, --mirgenedb_mature and --mirgenedb_hairpin

Species for miRTrace.

type: string

This is automatically set when using --genome. Example values: hsa, mmu...
Note that mirTrace relies on miRBase for its species reference. See available references here.

Species of MirGeneDB.

type: string

This replaces the value of --mirtrace_species if --mirgenedb is used.
Note the difference in case for species names used in MirGeneDB and miRBase. See https://www.mirgenedb.org/browse for more information.

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

GFF/GTF file with coordinates positions of precursor and miRNAs.

type: string

miRBase .gff3 file, typically downloaded from https://mirbase.org/download/CURRENT/genomes/

If using iGenomes with --genome this file will be downloaded from miRBase automatically during the pipeline run.

GFF/GTF file with coordinates positions of precursor and miRNAs.

type: string

MirGeneDB .gff3 file, typically downloaded from [https://mirgenedb.org/download]. This replaces the value of --mirna_gff if --mirgenedb is used.

Path to FASTA file with mature miRNAs.

type: string
default: https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.fa

Typically this will be the mature.fa file from miRBase. Can be given either as a plain text .fa file or a compressed .gz file.

Defaults to the current miRBase release URL, from which the file will be downloaded.

Path to FASTA file with MirGeneDB mature miRNAs.

type: string

This file needs to be downloaded from [https://mirgenedb.org/download]. Can be given either as a plain text .fa file or a compressed .gz file.

Path to FASTA file with miRNAs precursors.

type: string
default: https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa

Typically this will be the mature.fa file from miRBase. Can be given either as a plain text .fa file or a compressed .gz file.

Defaults to the current miRBase release URL, from which the file will be downloaded.

Path to FASTA file with miRNAs precursors.

type: string

This file needs to be downloaded from [https://mirgenedb.org/download]. Can be given either as a plain text .fa file or a compressed .gz file.
Note that MirGeneDB does not have a dedicated hairpin file. The equivalent is the Precursor sequences.

Path to a Bowtie 1 index directory

type: string

Point to the directory created by Bowtie 1 when indexing. Bowtie 1 indices consist of six files:

genome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt  

Save generated reference genome files to results.

type: boolean

Saving generated references means that you can use them for future pipeline runs, reducing processing times.

Do not load the iGenomes reference config.

hidden
type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

Options for trimming reads and primers.

The number of basepairs to remove from the 5' end of read 1.

type: integer

The number of basepairs to remove from the 3' end of read 1 AFTER adapter/quality trimming has been performed.

type: integer

Sequencing adapter sequence to use for trimming.

type: string
default: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

Trim FastQ files

type: boolean
default: true

Minimum filter length for raw reads.

type: integer
default: 17

Maximum filter length for raw reads.

type: integer
default: 100

Save reads failing trimming

type: boolean

Fasta with known miRNA adapter sequences for adapter trimming

type: string
default: ${projectDir}/assets/known_adapters.fa

Minimum number of reads required in input file to use it

type: integer
default: 10

Save merged reads.

type: boolean

The PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format.

type: integer
default: 33

Options to remove contamination from the reads.

Enables the contamination filtering.

type: boolean

Path to the rRNA fasta file to be used as contamination database.

type: string

Path to the tRNA fasta file to be used as contamination database.

type: string

Path to the cDNA fasta file to be used as contamination database.

type: string

Path to the ncRNA fasta file to be used as contamination database.

type: string

Path to the piRNA fasta file to be used as contamination database.

type: string

Path to an additional fasta file to be used as contamination database.

type: string

Switches to skip specific pipeline steps, if desired.

Skip FastQC

type: boolean

Skip miRDeep

type: boolean

Skip MultiQC

type: boolean

Skip FastP

type: boolean

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
default: true

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.

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

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