Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
stringYou 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.
Path to a local or remote directory that is the "current working directory" for relative paths defined in the input samplesheet
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string./resultsEmail address for completion summary.
stringSet 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.
Trim N bases from the front of the reads
integerTrim N bases from the tail of the reads
integerThe maximum length of a read
integerReads longer then given length will be trimmed to the given length. If you set this argument it will overrule the value from the chosen design
The minimum length (bases) of a read
integerReads shorter then given length will be discarded. If you set this argument it will overrule the value from the chosen design.
The maximum number of Ns allowed in a read
integerThe default value of 0 means any reads with N in it will be filtered out
Minimum avg. quality a read must have (0 will disable the filter)
integer20Remove duplicated reads (exact same sequence)
booleanRemove PolyG sequences (length of 10 or more)
booleanThe number of mismatches allowed (in percentage) [default: 0.1; 0.0<=x<=0.9]
number0.1The number of mismatches allowed (as a fraction)
number0.1The minimum length of the barcode that must overlap when matching
integerIf you set this argument it will overrule the value from the chosen design
A list of comma separated antibodies to discard
stringThe algorithm to use for collapsing (adjacency will peform error correction using the number of mismatches given)
stringThe maximum number of neighbors to use when searching for similar sequences. This number depends on the sequence depth and the ratio of erroneous molecules expected. A high value can make the algorithm slower. This is only used when algorithm is set to 'adjacency'
integer60The number of mismatches allowed when collapsing (adjacency)
integer2Discard molecules with with a count (reads) lower than this value
integer2Use counts when collapsing (the difference in counts between two molecules must be more than double in order to be collapsed)
booleanActivate the multiplet recovery using leiden community detection
booleantrueNumber of iterations for the leiden algorithm, high values will decrease the variance of the results but increase the runtime [default: 10; 1<=x<=100]
integer10Discard edges (pixels) with a count (reads) lower than this, use 1 to disable
integer2The minimum size (pixels) a component/cell can have (disabled by default)
integerThe maximum size (pixels) a component/cell can have (disabled by default)
integerEnable the estimation of dynamic size filters using a log-rank approach both: estimate both min and max size, min: estimate min size (--min-size), max: estimate max size (--max-size)
stringEnable aggregate calling, information on potential aggregates will be added to the output data
booleantrueSkip analysis step
booleanCompute polarization scores matrix (clusters by markers)
booleantrueCompute colocalization scores (marker by marker) for each component
booleantrueUse the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores
booleanWhich approach to use to normalize the antibody counts.
string-
raw: use the raw counts. -
CLR: use the CLR-transformed counts. -
denoise: use CLR-transformed counts and subtract the counts of control antibodies
Transform the antibody counts to 0-1 (binarize) when computing polarization
booleanSelect the type of transformation to use on the node by antibody counts matrix when computing colocalization
stringSelect the size of the neighborhood to use when computing colocalization metrics on each component
integer1Set the number of permutations use to compute the empirical p-value for the colocalization score
integer50The minimum number of counts in a region for it to be concidered valid for computing colocalization
integer5Skip report generation
booleanGlobal configuration options specific to nf-core/pixelator.
Override the container image reference to use for all steps using the pixelator command.
stringUse this to force the pipeline to use a different image version in all steps that use the pixelator command.
The pipeline is not garanteed to work when using different pixelator versions.
Parameters 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.GBUse 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.hUse 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.
stringAn 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.
Directory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean 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.