nf-core/smrnaseq
A small-RNA sequencing analysis pipeline
2.0.0). The latest
stable release is
2.4.0
.
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$Protocol for constructing smRNA-seq libraries.
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
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.
stringhttps://mirbase.org/ftp/CURRENT/mature.fa.gzPath to FASTA file with miRNAs precursors.
stringhttps://mirbase.org/ftp/CURRENT/hairpin.fa.gzPath to a Bowtie 1 index directory
stringSave generated reference genome files to results.
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanOptions for trimming reads and primers.
Discard reads that are shorter than this after quality / adapter trimming.
integer17The 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.
stringTGGAATTCTCGGGTGCCAAGGThe miRTrace protocol for QC reporting.
stringThe max-length parameter used for trimming with TrimGalore!.
integer40Switches to skip specific pipeline steps, if desired.
Skip all QC steps
booleanSkip FastQC
booleanSkip miRDeep
booleanSkip MultiQC
booleanSkip all trimming steps.
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.
stringSet 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$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
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.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean