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: integer
default: 5000

Minimum block length filter for mapping.

type: string
default: wfmash_segment_length * 5

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: number
default: 1.0

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. [default: all-vs-all and !self].

hidden
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

Ignores exact matches below this length.

type: integer
default: 19

Number of base pairs to use for transitive closure batch.

type: integer
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:DELIM[,REF:DELIM:[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

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

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$

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*)+$

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

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

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean

Do we want to display hidden parameters?

hidden
type: boolean

Do we want to display hidden parameters?

hidden
type: string
default: igenomes_base