Filters to decide which observation to run

Pulsar name for PSRDB search. Returns only observations with this pulsar name.

type: string

Start UTC for PSRDB search. Returns only observations after this UTC timestamp.

type: string

End UTC for PSRDB search. Returns only observations before this UTC timestamp.

type: string

Project short name (e.g. PTA) for PSRDB search. Return only observations matching this Project short code.

type: string

Path to CSV file containing the observations to process in the format described in the documentation

type: string

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

Base directory of input archive files

type: string
default: /fred/oz005/timing

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

type: string
default: /fred/oz005/timing_processed

Path to the ephemris which will overwrite the default described above. Recommended to only be used for single observations.

type: string

Path to the template which will overwrite the default described above. Recommended to only be used for single observations.

type: string

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.

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type: string

Options to change the pipeline logic

Use first and last 8 second subints of observation archives.

type: boolean

Remove edge frequency channels of the archive before decimating.

type: boolean
default: true

Instead of creating a single time scrunched ToA, created as many as possible based on the S/N ration and observation length.

type: boolean
default: true

Use the previously created calibrated and cleaned archive in the output directory.

type: boolean

Desired ToA S/N ratio, used to calculate the nsub to use

type: integer
default: 12

Comma separated list of nchans to frequency scrunch the data into

type: string
default: 1,16,32,58,116,928

Comma separated list of number of polarisations to scrunch the data into..

type: string
default: 1,4

Maximum number of channels of residuals to upload. Large number of channels slows down the upload and are often not required.

type: integer
default: 32

Options for interacting with the meertime dataportal pulsars.org.au

Upload result to the database

type: boolean
default: true

URL for interacting with the database API. Can be set with the $PSRDB_URL environment variable.

type: string

Token taken from environment variable and obtained using get_ingest_token.sh or get_token.sh. Can be set with the $PSRDB_TOKEN environment variable.

type: string

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

Git commit id for Institutional configs.

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type: string
default: master

Base directory for Institutional configs.

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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.

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type: string

Institutional config description.

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type: string

Institutional config contact information.

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type: string

Institutional config URL link.

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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.

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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.

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type: string
default: 250.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.

type: boolean

Display help text.

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type: boolean

Display version and exit.

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type: boolean

Method used to save pipeline results to output directory.

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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.

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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.

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type: boolean

Do not use coloured log outputs.

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type: boolean

Incoming hook URL for messaging service

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type: string

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

Boolean whether to validate parameters against the schema at runtime

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type: boolean
default: true
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type: boolean
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type: string
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type: string
default: genomes,validationSchemaIgnoreParams,manifest,validation-schema-ignore-params
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type: string
default: /fred/oz005/timing_processed/pipeline_info
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type: boolean