nf-core/smrnaseq
A small-RNA sequencing analysis pipeline
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
^\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.
string
Email address for completion summary.
string
^([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.
string
Save all intermediate files (e.g. fastq, bams) to output directory
boolean
Options for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
boolean
UMI pattern to use. Can be either 'string' (default) or 'regex'.
string
string
More details can be found in the UMI-tools documentation.
UMI grouping method
string
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.
boolean
true
The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.
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.
integer
If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
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
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.
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.
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.
string
^\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.
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.
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.
string
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.
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.
string
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.
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
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.
boolean
Saving generated references means that you can use them for future pipeline runs, reducing processing times.
Do not load the iGenomes reference config.
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.
integer
The number of basepairs to remove from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
integer
Sequencing adapter sequence to use for trimming.
string
AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
Trim FastQ files
boolean
true
Minimum filter length for raw reads.
integer
17
Maximum filter length for raw reads.
integer
100
Save reads failing trimming
boolean
Fasta with known miRNA adapter sequences for adapter trimming
string
${projectDir}/assets/known_adapters.fa
Minimum number of reads required in input file to use it
integer
10
Save merged reads.
boolean
The PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format.
integer
33
Options to remove contamination from the reads.
Enables the contamination filtering.
boolean
Path to the rRNA fasta file to be used as contamination database.
string
Path to the tRNA fasta file to be used as contamination database.
string
Path to the cDNA fasta file to be used as contamination database.
string
Path to the ncRNA fasta file to be used as contamination database.
string
Path to the piRNA fasta file to be used as contamination database.
string
Path to an additional fasta file to be used as contamination database.
string
Switches to skip specific pipeline steps, if desired.
Skip FastQC
boolean
Skip miRDeep
boolean
Skip MultiQC
boolean
Skip FastP
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
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.
string
240.h
^(\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.
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
^([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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
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
true
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.
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/