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$
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})$
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Save all intermediate files (e.g. fastq, bams) of all steps of the pipeline 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
UMI grouping method
string
dir
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
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
Boolean whether MirGeneDB should be used instead of miRBase
boolean
Species for miRTrace.
string
Species of MirGeneDB.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
GFF/GTF file with coordinates positions of precursor and miRNAs.
string
GFF/GTF file with coordinates positions of precursor and miRNAs.
string
Path to FASTA file with mature miRNAs.
string
https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.fa
Path to FASTA file with MirGeneDB mature miRNAs.
string
Path to FASTA file with miRNAs precursors.
string
https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa
Path to FASTA file with miRNAs precursors.
string
Path to a Bowtie 1 index directory
string
Save generated reference genome files to results.
boolean
Do not load the iGenomes reference config.
boolean
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
${projectDir}/assets/known_adapters.fa
Minimum number of reads required in input file to use it
integer
10
Save merged reads.
boolean
The PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format.
integer
33
Options to remove contamination from the reads.
Enables the contamination filtering.
boolean
Path to the rRNA fasta file to be used as contamination database.
string
Path to the tRNA fasta file to be used as contamination database.
string
Path to the cDNA fasta file to be used as contamination database.
string
Path to the ncRNA fasta file to be used as contamination database.
string
Path to the piRNA fasta file to be used as contamination database.
string
Path to an additional fasta file to be used as contamination database.
string
Switches to skip specific pipeline steps, if desired.
Skip FastQC
boolean
Skip miRDeep
boolean
Skip MultiQC
boolean
Skip FastP
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
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
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
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/