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$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

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 for DESeq2.

type: string
pattern: \.csv$

There are two rules for providing the phenotype CSV file. 1) The phenotype 'sample' column must match the sample sheets 'sample' column. 2) The response variable containing the phenotype of primary interest in the experiment must have the column name condition. All other columns included in the file are controlled for in the DESeq2 design.

| sample | condition | replicate |
|----------- |----------- |----------- |
| control_1 | ctr | 1 |
| control_2 | ctr | 2 |
| control_3 | ctr | 3 |
| treated_1 | trt | 1 |
| treated_2 | trt | 2 |
| treated_3 | trt | 3 |

The above phenotype file will identify differentially expressed circRNAs/mRNAs between control and treatment cells, whilst controlling for the effect of variation between replicates: ~ replicates + condition

Main workflow parameters.

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
pattern: ^((circexplorer2|circrna_finder|ciriquant|dcc|find_circ|mapsplice|segemehl)?,?)*[^,]+$

Select one or a combination of circRNA quantification tools for the pipeline e.g:
--tool 'circexplorer2, ciriquant, find_circ'

N.B: Selecting more than one circRNA quantification tool will trigger the circRNA filtering parameter --tool_filter

Comma separated list of modules to run: 'circrna_discovery', 'mirna_prediction' & 'differential_expression'.

required
type: string
default: circrna_discovery
pattern: ^((circrna_discovery|mirna_prediction|differential_expression)?,?)*[^,]+$

The 'circrna_discovery' module is mandatory. After circRNA quantification, the user can select 'mirna_prediction', 'differential_expression' or both to deploy additional analyses e.g:
--module 'circrna_discovery, mirna_prediction, differential_expression'

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

type: integer

Filter low confidence circRNAs by removing circRNAs with read counts below a specified value. To disable, set the value to 0 (default).

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

type: integer

When multiple circRNA quantification tools have been provided to --tool, set a filtering method whereby circRNAs are output if they have been called by at least n quantification tools.

Setting --tool_filter to 0/1 is the same as taking the union, all circRNAs are included in the output.

Setting --tool_filter to 2 will output circRNAs that have been called by at least 2 quantification tools and so on.

Please note this is only reflected in the circRNA count matrix generated.

Aggregate function to apply to duplicate circRNAs when more than one quantification tool has been selected. Options: max, mean

type: string

Save intermediate alignment/circRNA files.

type: boolean

Specify the distance at which the annotation script decides if a candidate is a circRNA or EI-circRNA.

type: integer
default: 200

During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 200bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs.

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

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

This may either be in the form of FastQ or BAM files depending on the options available for that particular tool.

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

By using a reference genome build on iGenomes, the gtf, mature, species and index files (bar HISAT2 and segemehl) will be automatically downloaded for you.

See the nf-core website docs for more details.

Path to FASTA genome file.

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

If you use AWS iGenomes, this has already been set for you appropriately.

This parameter is mandatory if --genome is not specified.

Path to reference GTF file.

type: string
pattern: \.gtf$

Path to FASTA file with mature miRNAs.

type: string

Typically this will be the mature.fa file from miRBase. Can be given either as a plain text .fa file or a compressed .gz file.

String identifying species.

type: string

Check the igenomes.config file for species configured to work with nf-core/circrna

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$

HiSAT2 requires a huge amount of RAM to build a genome index for larger genomes, if including splice sites and exons e.g. the human genome might typically require 200GB. If you specify less than this threshold for the HISAT2_BUILD process then the splice sites and exons will be ignored, meaning that the process will require a lot less memory. If you are working with a small genome, set this parameter to a lower value to reduce the threshold for skipping this check. If using a larger genome, consider supplying more memory to the HISAT2_BUILD process.

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

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

Options to adjust read trimming criteria.

Skip the adapter trimming step.

type: boolean

Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.

Save the trimmed FastQ files in the results directory.

type: boolean

By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.

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

This enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 50

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 300.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

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

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

Email address for completion summary.

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

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

Send plain-text email instead of HTML.

hidden
type: boolean

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

Show all params when using --help

hidden
type: boolean

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.