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.
string
Phenotype 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.
string
Parameters 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
string
circexplorer2
Minimum number of reads spanning circRNA back-splice junction required for circRNA to be output by workflow.
integer
1
If both start and end of a pair of BSJs are within max_shift bp, they are considered as the same BSJ.
integer
Consider strand information when comparing BSJs.
boolean
true
Specify the minimum number of tools circRNAs must be called by to be output by the workflow.
integer
1
Minimum number of samples a circRNA must be detected in to be output by the workflow.
integer
1
Only consider exons for circRNA sequence extraction.
boolean
true
Enable the detection of full-length isoforms (FLI). This requires paired-end reads.
boolean
true
Parameters for circRNA quantification.
Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, psirc
string
ciriquant,psirc,sum,max
^((ciriquant|psirc|sum|max)(,(ciriquant|psirc|sum|max))*)+$
Number of bootstrap samples to use during psirc quantification.
integer
30
Define 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.
number
0.2
Minimum number of reads, a miRNA is required to have to pass filtering.
integer
5
Specifies the type of correlation to be used when analyzing the relationship between miRNA and transcript expression levels. Valid options are ‘pearson’ or ‘spearman’.
string
pearson
Comma separated list of miRNA bindingsite prediction tools to use. Supported tools: miranda, targetscan.
string
miranda,targetscan
^((miranda|targetscan)?,?)*[^,]+$
Specify the number of votes required for a miRNA to be further considered in downstream analysis.’
integer
1
Parameters 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.
integer
100
Minimum overhang for a chimeric junction
integer
10
Minimum overhang for annotated junctions
integer
10
Maximum 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
integer
1000000
Minimum length of chimeric segment length. Must be set to a positive value to detect circular junctions.
integer
10
Segment length. Default 25
integer
25
Minimum intron length. Default 20
integer
20
Maximum intron length. Default 1000000
integer
1000000
Minimum alignment length. Default 40
integer
40
Minimum 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).
integer
200
Sequencing center information to be added to read group of BAM files.
string
Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
boolean
Reference genome related files and options required for the workflow.
Save generated reference genome files such as indices, chromosome FASTA files.
boolean
true
Name of iGenomes reference.
string
Path 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.
string
Path to Bowtie index files, surrounded by quotes. No glob pattern required.
string
Path to Bowtie2 index files, surrounded by quotes. No glob pattern required.
string
Path to BWA index directory, surrounded by quotes. No glob pattern required.
string
Path to Hisat2 index directory, surrounded by quotes. No glob pattern required.
string
Minimum memory required to use splice sites and exons in the HiSAT2 index build process.
string
200.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Path to Segemehl Index file.
string
Path to STAR index directory, surrounded by quotes. No glob pattern required.
string
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Options to adjust read trimming criteria.
Skip the adapter trimming step.
boolean
Save the trimmed FastQ files in the results directory.
boolean
Skip FastQC quality control of the sequencing reads.
boolean
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integer
Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integer
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integer
Minimum 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.
integer
10000
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
Save intermediate files.
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/
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string