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.

Fasta file of primers sequences

required
type: string

The provided file must contains all primers sequences used for sequencing.
Gziped files are accepted.

Genome annotation file

type: string

Provide a GTF annotation file (sorted by sequence and start) if you set the --aligner option to uLTRA
Gziped files are accepted.

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

required
type: string
default: null

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.

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

type: string

Use these options to set CCS parameters

ccs --chunk option, define the number of batches to run in parallel

type: integer
default: 40

CCS workload can be split into to chunks for a faster running time.
This value must be a positive integer greater than 1.

--chunk 1/10   

ccs --rq option, define the minimum read quality for CCS selection

type: number
default: 0.9

Minimum read quality for a consensus.
Under this threshold the sequence is discarded.
This value must be in range [0-1].

--rq 0.9  

ccs --min-passes option, define the minimum number of passes to select a CCS

type: integer
default: 3

Minimum number of full-length subreads required to generate CCS for a ZMW.

ccs --min-snr option, minimum SNR of subreads to use for generating CCS

type: number
default: 2.5

Minimum SNR of subreads to use for generating CCS

ccs --min-length option, minimum CCS length for CCS selection

type: integer
default: 10

Minimum draft length before polishing

ccs --max-length option, maximum CCS length for CCS selection

type: integer
default: 50000

Maximum draft length before polishing

ccs --top-passes option, maximum number of passes to use for CCS generation

type: integer
default: 60

Pick at maximum the top N passes for each ZMW

Aligner selection

Aligner to use for mapping: minimap2 or ultra

required
type: string

The uLTRA aligner improve detection of small exons but require an annotation in GTF format to run.
If the genome don't have any reference annotation, you have to use minimap2.

Use these options to set TAMA collapse and TAMA merge parameters

TAMA collapse: Capped RNA?

type: boolean

Set this option if the RNAs are capped.

--capped  

TAMA collapse: 5 prime wobble threshold

type: integer
default: 100

Set the maximum threshold for collapsing 5 prime exon.

--five_prime 100  

TAMA collapse: Splice junction / exon wobble threshold

type: integer
default: 10

Set the maximum threshold for collapsing spliced exons.

--splice_junction 10  

TAMA collapse: 3 prime wobble threshold

type: integer
default: 100

Set the maximum threshold for collapsing 3 prime exon.

--three_prime 100  

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Path to FASTA genome file.

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

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs. Gziped files are accepted.

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.

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: 16

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: 128.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, 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

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.

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

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/