nf-core/circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringPhenotype CSV file specifying the experimental design. If provided, the pipeline will run CIRCTEST.
string^\S+\.csv$Path to a CSV file containing BED files that should be used for annotation.
string^\S+\.csv$Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters for back-splice junction detection.
Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, circexplorer2, find_circ, circrna_finder, mapsplice, dcc, segemehl
stringcircexplorer2Minimum number of reads spanning circRNA back-splice junction required for circRNA to be output by workflow.
integer1If both start and end of a pair of BSJs are within max_shift bp, they are considered as the same BSJ.
integerConsider strand information when comparing BSJs.
booleantrueSpecify the minimum number of tools circRNAs must be called by to be output by the workflow.
integer1Minimum number of samples a circRNA must be detected in to be output by the workflow.
integer1Only consider exons for circRNA sequence extraction.
booleantrueEnable the detection of full-length isoforms (FLI). This requires paired-end reads.
booleantrueParameters for circRNA quantification.
Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, psirc
stringciriquant,psirc,sum,max^((ciriquant|psirc|sum|max)(,(ciriquant|psirc|sum|max))*)+$Number of bootstrap samples to use during psirc quantification.
integer30Define paths and threasholds for miRNA analysis.
path to tab-separated file providing the expression counts of mirnas, which are created in pipeline ‘smrnaseq’.
mirna sample1 sample2 sample3 id1 count_sample1 count_sample2 count_sample3 id2 … … …
string^\S+\.tsv$Minimum percentage of samples, a miRNA has to be expressed in to pass filtering.
number0.2Minimum number of reads, a miRNA is required to have to pass filtering.
integer5Specifies the type of correlation to be used when analyzing the relationship between miRNA and transcript expression levels. Valid options are ‘pearson’ or ‘spearman’.
stringpearsonComma separated list of miRNA bindingsite prediction tools to use. Supported tools: miranda, targetscan.
stringmiranda,targetscan^((miranda|targetscan)?,?)*[^,]+$Specify the number of votes required for a miRNA to be further considered in downstream analysis.’
integer1Parameters used by aligners pertinent to circRNA detection
only used at the genome generation step tells STAR how many bases to concatenate from donor and acceptor sides of the junctions.
integer100Minimum overhang for a chimeric junction
integer10Minimum overhang for annotated junctions
integer10Maximum number of junction to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run
integer1000000Minimum length of chimeric segment length. Must be set to a positive value to detect circular junctions.
integer10Segment length. Default 25
integer25Minimum intron length. Default 20
integer20Maximum intron length. Default 1000000
integer1000000Minimum alignment length. Default 40
integer40Minimum distance between two gapped segments to be considered as fusion candidate. Must set to lower values to be sensitive to circular candidates (e.g 200).
integer200Sequencing center information to be added to read group of BAM files.
stringWhere possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
booleanReference genome related files and options required for the workflow.
Save generated reference genome files such as indices, chromosome FASTA files.
booleantrueName of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to reference GTF file.
string\.gtf$Path to blacklist bed file.
string^\S+\.bed$Path to FASTA file with mature miRNAs. This parameter needs to be specified to perform miRNA interaction analyses.
stringPath to Bowtie index files, surrounded by quotes. No glob pattern required.
stringPath to Bowtie2 index files, surrounded by quotes. No glob pattern required.
stringPath to BWA index directory, surrounded by quotes. No glob pattern required.
stringPath to Hisat2 index directory, surrounded by quotes. No glob pattern required.
stringMinimum memory required to use splice sites and exons in the HiSAT2 index build process.
string200.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Path to Segemehl Index file.
stringPath to STAR index directory, surrounded by quotes. No glob pattern required.
stringDo not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Options to adjust read trimming criteria.
Skip the adapter trimming step.
booleanSave the trimmed FastQ files in the results directory.
booleanSkip FastQC quality control of the sequencing reads.
booleanInstructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integerInstructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integerInstructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integerMinimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.
integer10000Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanSave intermediate files.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string