nf-core/molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
Define which segmentation methods should be used and how.
List of segmentation tools to apply to the image written as a comma separated string: mesmer,cellpose,ilastik would run all three options.
stringmesmerMinimum area size (in pixels) for segmentation masks.
integerMaximum area size (in pixels) for segmenation masks.
integerCell diameter, if 0 will use the diameter of the training labels used in the model, or with built-in model will estimate diameter for each image.
integer30Specifies the channel to be segmented by Cellpose.
integerSpecifies nuclear channel index for Cellpose if using pretrained models such as cyto.
integerPretrained Cellpose model to be used for segmentation.
stringcytoCustom Cellpose model can be provided by the user.
stringFlow error threshold for Cellpose.
number0.4Should cells detected near image edges be excluded.
booleantrueShould flow fields from Cellpose be saved?
booleanPixel size in microns for segmentation with Mesmer.
number0.138Compartment to be segmented with Mesmer (nuclear, whole-cell)
stringwhole-cellProvide ilastik with a pixel classification project to produce probability maps.
stringProvide ilastik with a multicut project to create segmentation masks.
stringDefines gridsize for Mindagap and should contrast adjustment be applied and how.
Box size used by Mindagap to overcome gaps, a larger number allows to overcome large gaps, but results in less fine details in the filled grid.
integer3Loop number performed by Mindagap. Lower values are faster, but the result is less good.
integer40Contrast limit for localized changes in contrast by CLAHE.
number0.01Number of histogram bins to be used by CLAHE.
integer256Pixel size to be used by CLAHE.
number0.138Kernel size to be used by CLAHE.
number25Specifies whether contrast-limited adaptive histogram equalization should be skipped.
booleanTile size (distance between gridlines) for Mindagap.
integer2144Should Mindagap blur area around grid for smoother transitions between tiles with different exposures.
booleanTile size used for pyramid generation (must be divisible by 16).
integer1072Define whether a cropped training set for segmentation methods should be created.
Create subset for training a segmentation model.
booleanIndicates crop size on x axis.
integer400Indicates crop size on y axis.
integer400Number of crops you would like to extract.
integer4Indicates fraction of pixels per crop above global threshold to ensure tissue and not only background is selected.
number0.4Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
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.
string128.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.
Display 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/