nf-core/pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
1.1.0). The latest
stable release is
2.0.0
.
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.
string^\S+\.(csv|tsv)$Path to a local or remote directory that is the “current working directory” for relative paths defined in the input samplesheet
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Trim N bases from the front of the reads
integerTrim N bases from the tail of the reads
integerThe maximum length of a read
integerThe minimum length (bases) of a read
integerThe maximum number of Ns allowed in a read
integerMinimum 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
integerA list of comma separated antibodies to discard
string(\S+)?(,\S+)*The algorithm to use for collapsing (adjacency will perform 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.
stringTransform 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 considered 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.
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/masterInstitutional 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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
boolean