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.

required
type: string
pattern: ^\S+\.csv$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Phenotype CSV file specifying the experimental design. If provided, the pipeline will run CIRCTEST.

type: string
pattern: ^\S+\.csv$

Path to a CSV file containing BED files that should be used for annotation.

type: string
pattern: ^\S+\.csv$

Email address for completion summary.

type: string
pattern: ^([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.

type: 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

required
type: string
default: circexplorer2

Minimum number of reads spanning circRNA back-splice junction required for circRNA to be output by workflow.

type: integer
default: 1

If both start and end of a pair of BSJs are within max_shift bp, they are considered as the same BSJ.

type: integer

Consider strand information when comparing BSJs.

type: boolean
default: true

Specify the minimum number of tools circRNAs must be called by to be output by the workflow.

type: integer
default: 1

Minimum number of samples a circRNA must be detected in to be output by the workflow.

type: integer
default: 1

Only consider exons for circRNA sequence extraction.

type: boolean
default: true

Enable the detection of full-length isoforms (FLI). This requires paired-end reads.

type: boolean
default: true

Parameters for circRNA quantification.

Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, psirc

required
type: string
default: ciriquant,psirc,sum,max
pattern: ^((ciriquant|psirc|sum|max)(,(ciriquant|psirc|sum|max))*)+$

Number of bootstrap samples to use during psirc quantification.

type: integer
default: 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 … … …

type: string
pattern: ^\S+\.tsv$

Minimum percentage of samples, a miRNA has to be expressed in to pass filtering.

type: number
default: 0.2

Minimum number of reads, a miRNA is required to have to pass filtering.

type: integer
default: 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’.

type: string
default: pearson

Comma separated list of miRNA bindingsite prediction tools to use. Supported tools: miranda, targetscan.

type: string
default: miranda,targetscan
pattern: ^((miranda|targetscan)?,?)*[^,]+$

Specify the number of votes required for a miRNA to be further considered in downstream analysis.’

type: integer
default: 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.

type: integer
default: 100

Minimum overhang for a chimeric junction

type: integer
default: 10

Minimum overhang for annotated junctions

type: integer
default: 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

type: integer
default: 1000000

Minimum length of chimeric segment length. Must be set to a positive value to detect circular junctions.

type: integer
default: 10

Segment length. Default 25

type: integer
default: 25

Minimum intron length. Default 20

type: integer
default: 20

Maximum intron length. Default 1000000

type: integer
default: 1000000

Minimum alignment length. Default 40

type: integer
default: 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).

type: integer
default: 200

Sequencing center information to be added to read group of BAM files.

type: string

Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.

type: boolean

Reference genome related files and options required for the workflow.

Save generated reference genome files such as indices, chromosome FASTA files.

type: boolean
default: true

Name of iGenomes reference.

type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Path to reference GTF file.

type: string
pattern: \.gtf$

Path to blacklist bed file.

type: string
pattern: ^\S+\.bed$

Path to FASTA file with mature miRNAs. This parameter needs to be specified to perform miRNA interaction analyses.

type: string

Path to Bowtie index files, surrounded by quotes. No glob pattern required.

type: string

Path to Bowtie2 index files, surrounded by quotes. No glob pattern required.

type: string

Path to BWA index directory, surrounded by quotes. No glob pattern required.

type: string

Path to Hisat2 index directory, surrounded by quotes. No glob pattern required.

type: string

Minimum memory required to use splice sites and exons in the HiSAT2 index build process.

type: string
default: 200.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Path to Segemehl Index file.

type: string

Path to STAR index directory, surrounded by quotes. No glob pattern required.

type: string

Do not load the iGenomes reference config.

hidden
type: boolean

The base path to the igenomes reference files

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Options to adjust read trimming criteria.

Skip the adapter trimming step.

type: boolean

Save the trimmed FastQ files in the results directory.

type: boolean

Skip FastQC quality control of the sequencing reads.

type: boolean

Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).

type: integer

Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.

type: 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.

type: integer
default: 10000

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Less common options for the pipeline, typically set in a config file.

Display version and exit.

hidden
type: boolean

Save intermediate files.

type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: 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.

hidden
type: string