nf-core/smrnaseq
A small-RNA sequencing analysis pipeline
1.1.0). The latest
stable release is
2.4.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files.
stringProtocol for constructing smRNA-seq libraries.
stringThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Options for the reference genome indices used to align reads.
Name of iGenomes reference.
stringSpecies for miRTrace.
stringPath to reference genome FASTA genome file.
stringGFF/GTF file with coordinates positions of precursor and miRNAs.
stringPath to FASTA file with mature miRNAs.
stringftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gzPath to FASTA file with miRNAs precursors.
stringftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gzPath to the Bowtie 1 reference genome index.
stringPath to the parsed reference folder containing the files for the miRDeep2.
stringSave generated reference genome files to results.
booleantrueDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanList of bowtie index files
arrayDiscard reads that are shorter than this after quality / adapter trimming.
integer17Bp to remove from the 5’ end of read 1
integerBp to remove from the 3’ end of read 1 AFTER adapter/quality trimming has been performed
integerSequencing adapter sequence to search for and remove.
stringTGGAATTCTCGGGTGCCAAGGprotocol to be used for the mirtrace process
stringtrimgalore max-length parameter
integer40Skip all QC steps
booleanSkip FastQC
booleanSkip miRDeep
booleanSkip MultiQC
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueText about sequencing center which will be added in the header of output bam files.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Parameters 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 configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string