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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSave all intermediate files (e.g. fastq, bams) of all steps of the pipeline to output directory
booleanOptions for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
booleanUMI pattern to use. Can be either ‘string’ (default) or ‘regex’.
stringstringUMI grouping method
stringdirSkip 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.
booleantrueThe UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.
stringAfter UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.
integerIf this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringBoolean whether MirGeneDB should be used instead of miRBase
booleanSpecies for miRTrace.
stringSpecies of MirGeneDB.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$GFF/GTF file with coordinates positions of precursor and miRNAs.
stringGFF/GTF file with coordinates positions of precursor and miRNAs.
stringPath to FASTA file with mature miRNAs.
stringhttps://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.faPath to FASTA file with MirGeneDB mature miRNAs.
stringPath to FASTA file with miRNAs precursors.
stringhttps://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.faPath to FASTA file with miRNAs precursors.
stringPath to a Bowtie 1 index directory
stringSave generated reference genome files to results.
booleanDo not load the iGenomes reference config.
booleanOptions for trimming reads and primers.
The number of basepairs to remove from the 5’ end of read 1.
integerThe number of basepairs to remove from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integerSequencing adapter sequence to use for trimming.
stringAGATCGGAAGAGCACACGTCTGAACTCCAGTCATrim FastQ files
booleantrueMinimum filter length for raw reads.
integer17Maximum filter length for raw reads.
integer100Save reads failing trimming
booleanFasta with known miRNA adapter sequences for adapter trimming
string${projectDir}/assets/known_adapters.faMinimum number of reads required in input file to use it
integer10Save merged reads.
booleanThe PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format.
integer33Options to remove contamination from the reads.
Enables the contamination filtering.
booleanPath to the rRNA fasta file to be used as contamination database.
stringPath to the tRNA fasta file to be used as contamination database.
stringPath to the cDNA fasta file to be used as contamination database.
stringPath to the ncRNA fasta file to be used as contamination database.
stringPath to the piRNA fasta file to be used as contamination database.
stringPath to an additional fasta file to be used as contamination database.
stringSwitches to skip specific pipeline steps, if desired.
Skip FastQC
booleanSkip miRDeep
booleanSkip MultiQC
booleanSkip FastP
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/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/