User Parameters - Pipeline & job control

Here we detail the input parameters that cover the overall process control, and the switches to turn on & off different parts of the pipeline.

Values for parameters that act as flags (ie. those that accept true/false values) should be given in lower case only, to ensure comparisons work properly.

Slurm control

These parameters affect how the slurm jobs are set up and where the output data products go. To run the jobs, you need to set SUBMIT_JOBS=true.

Variable	Default	Description
SUBMIT_JOBS	false	The ultimate switch controlling whether things are run on the galaxy queue or not. If false, the slurm files etc will be created but nothing will run (useful for checking if things are to your liking).
CLUSTER	galaxy	The cluster to which jobs should be submitted. This allows you to submit to the galaxy queue from machines such as galaxy-data. Leave as is unless you konw better.
QUEUE	workq	This should be left as is unless you know better.
RESERVATION	“”	If there is a reservation you specify the name of it here. If you don’t have a reservation, leave this alone and it will be submitted as a regular job.
OUTPUT	.	The sub-directory in which to put the images, tables, catalogues, MSs etc. The name should be relative to the directory in which the script was run, with the default being that directory.
EMAIL	“”	An email address to which you want slurm notifications sent (this will be passed to the --mail-user option of sbatch). Leaving it blank will mean no notifications are sent.
EMAIL_TYPE	ALL	The types of notifications that are sent (this is passed to the --mail-type option of sbatch, and only if EMAIL is set to something). Options include: BEGIN, END, FAIL, REQUEUE, ALL, TIME_LIMIT, TIME_LIMIT_90, TIME_LIMIT_80, & TIME_LIMIT_50 (taken from the sbatch man page on galaxy).

Calibrator switches

These parameters control the different types of processing done on the calibrator observation. The three aspects are splitting by beam/scan, flagging, and finding the bandpass. The DO_1934_CAL acts as the “master switch” for the calibrator processing.

Variable	Default	Description
DO_1934_CAL	true	Whether to process the 1934-638 calibrator observations
DO_SPLIT_1934	true	Whether to split a given beam/scan from the input 1934 MS
DO_FLAG_1934	true	Whether to flag the splitted-out 1934 MS
DO_FIND_BANDPASS	true	Whether to fit for the bandpass using all 1934-638 MSs

Science field switches

These parameter control the different types of processing done on the science field, with DO_SCIENCE_FIELD acting as a master switch for the science field processing.

Variable	Default	Description
DO_SCIENCE_FIELD	true	Whether to process the science field observations
DO_SPLIT_SCIENCE	true	Whether to split out the given beam from the science MS
DO_FLAG_SCIENCE	true	Whether to flag the (splitted) science MS
DO_APPLY_BANDPASS	true	Whether to apply the bandpass calibration to the science observation
DO_AVERAGE_CHANNELS	true	Whether to average the science MS to continuum resolution
DO_CONT_IMAGING	true	Whether to image the science MS
DO_SELFCAL	false	Whether to self-calibrate the science data when imaging
DO_SOURCE_FINDING	false	Whether to do the source-finding with Selavy on the individual beam images and the final mosaic.
DO_MOSAIC	true	Whether to mosaic the individual beam images, forming a single, primary-beam-corrected image.
DO_COPY_SL	false	Whether to copy a channel range of the original full-spectral- resolution measurement set into a new MS.
DO_APPLY_CAL_SL	false	Whether to apply the gains calibration determined from the continuum self-calibration.
DO_CONT_SUB_SL	false	Whether to subtract a continuum model from the spectral-line dataset.
DO_SPECTRAL_IMAGING	false	Whether to do the spectral-line imaging