nf-core/meerpipe
nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
Filters to decide which observation to run
Pulsar name for PSRDB search. Returns only observations with this pulsar name.
stringStart UTC for PSRDB search. Returns only observations after this UTC timestamp.
stringEnd UTC for PSRDB search. Returns only observations before this UTC timestamp.
stringProject short name (e.g. PTA) for PSRDB search. Return only observations matching this Project short code.
stringPath to CSV file containing the observations to process in the format described in the documentation
stringDefine where the pipeline should find input data and save output data.
Base directory of input archive files
string/fred/oz005/timingThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string/fred/oz005/timing_processedPath to the ephemris which will overwrite the default described above. Recommended to only be used for single observations.
stringPath to the template which will overwrite the default described above. Recommended to only be used for single observations.
stringEmail address for completion summary.
string^([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.
stringOptions to change the pipeline logic
Use the previously created calibrated and cleaned archive in the output directory.
booleanUse first and last 8 second subints of observation archives.
booleanRemove edge frequency channels of the archive before decimating.
booleantrueAdditionally create decimations and ToAs with the mode nsub type (most common observation duration used for nsub length). Default True.
booleantrueAdditionally create decimations with the all nsub type (use all available nsubs). Default True.
booleantrueAdditionally create decimations and ToAs with the max nsub type (maximum number of nsubs with at least the 'toa_sn' signal-to-noise ratio). Default True.
booleantrueDesired ToA S/N ratio, used to calculate the max nsub type to use
integer12Comma separated list of nchans to frequency scrunch the data into
string1,16,32,58,116,928Comma separated list of number of polarisations to scrunch the data into..
string1,4Maximum number of channels of residuals to upload. Large number of channels slows down the upload and are often not required.
integer32Options for interacting with the meertime dataportal pulsars.org.au
Upload result to the database
booleantrueURL for interacting with the database API. Can be set with the $PSRDB_URL environment variable.
stringToken taken from environment variable and obtained using get_ingest_token.sh or get_token.sh. Can be set with the $PSRDB_TOKEN environment variable.
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string250.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
booleanDisplay help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
booleantruebooleanstringstringgenomes,validationSchemaIgnoreParams,manifest,validation-schema-ignore-paramsstring/fred/oz005/timing_processed/pipeline_infobooleanboolean