Define where the pipeline should find input data and save output data.

Path to BGZIPPED input FASTA to build the pangenome graph from.

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

The number of haplotypes in the input FASTA.

required
type: number

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

required
type: string

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

Options for the all versus all alignment phase.

Percent identity in the wfmash mashmap step.

type: number
default: 90

Segment length for mapping.

type: string
default: 5000

Minimum block length filter for mapping.

type: string

Kmer size for mashmap.

type: integer
default: 19

Ignore the top % most-frequent kmers.

type: number
default: 0.001

Keep this fraction of mappings (auto for giant component heuristic).

type: string
default: 1.0
pattern: (auto|[01]\.\d+)

Merge successive mappings.

type: boolean

Disable splitting of input sequences during mapping.

hidden
type: boolean

Skip mappings between sequences with the same name prefix before the given delimiter character. This can be helpful if several sequences originate from the same chromosome. It is recommended that the sequence names respect the https://github.com/pangenome/PanSN-spec. In future versions of the pipeline it will be required that the sequence names follow this specification.

type: string

Set the directory where temporary files should be stored. Since everything runs in containers, we don’t usually set this argument.

hidden
type: string

The number of files to generate from the approximate wfmash mappings to scale across a whole cluster. It is recommended to set this to the number of available nodes. If only one machine is available, leave it at 1.

type: integer
default: 1

If this parameter is set, only the wfmash alignment step of the pipeline is executed. This option is offered for users who want to run wfmash on a cluster.

type: boolean

Filter out mappings unlikely to be this Average Nucleotide Identity (ANI) less than the best mapping.

type: integer
default: 30

Number of mappings for each segment. [default: n_haplotypes - 1].

type: integer

Ignores exact matches below this length.

type: integer
default: 23

Number of base pairs to use for transitive closure batch.

type: string
default: 10000000

Keep this randomly selected fraction of input matches.

type: number

Set the directory where temporary files should be stored. Since everything runs in containers, we don’t usually set this argument.

hidden
type: string

Input PAF file. The wfmash alignment step is skipped.

type: string

Options for graph smoothing phase.

Skip the graph smoothing step of the pipeline.

type: boolean

Maximum path jump to include in the block.

hidden
type: integer

Maximum edge jump before a block is broken.

hidden
type: integer

Maximum sequence length to put int POA. Is a comma-separated list. For each integer, SMOOTHXG wil be executed once.

type: string
default: 700,900,1100

Minimum edit-based identity to cluster sequences.

hidden
type: string

Minimum ‘smallest / largest’ sequence length ration to cluster in a block.

hidden
type: integer

Path depth at which we don’t pad the POA problem.

type: integer
default: 100

Pad each end of each seuqence in POA with ‘smoothxg_poa_padding * longest_poa_seq’ base pairs.

type: number
default: 0.001

Score parameters for POA in the form of ‘match,mismatch,gap1,ext1,gap2,ext2’. It may also be given as presets: ‘asm5’, ‘asm10’, ‘asm15’, ‘asm20’. [default: 1,19,39,3,81,1 = asm5].

type: string
default: 1,19,39,3,81,1

Write MAF output representing merged POA blocks.

type: boolean

Use this prefix for consensus path names.

hidden
type: string
default: Consensus_

Set the directory where temporary files should be stored. Since everything runs in containers, we don’t usually set this argument.

hidden
type: string

Keep intermediate graphs during SMOOTHXG.

hidden
type: boolean

Run abPOA. [default: SPOA].

type: boolean

Run the POA in global mode. [default: local mode].

type: boolean

Number of CPUs for the potentially very memory expensive POA phase of SMOOTHXG. Default is ‘task.cpus’.

type: integer

Options for calling variants against reference(s).

Specify a set of VCFs to produce with --vcf_spec "REF[:LEN][,REF[:LEN]]*".

type: string

Options to run the partition algorithm for community detection.

Enable community detection.

type: boolean

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

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/

Do we want to display hidden parameters?

hidden
type: boolean

Do we want to display hidden parameters?

hidden
type: string
default: igenomes_base

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