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
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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
integer
Trim N bases from the tail of the reads
integer
The maximum length of a read
integer
The minimum length (bases) of a read
integer
The maximum number of Ns allowed in a read
integer
Minimum avg. quality a read must have (0 will disable the filter)
integer
20
Remove duplicated reads (exact same sequence)
boolean
Remove PolyG sequences (length of 10 or more)
boolean
The number of mismatches allowed (in percentage) [default: 0.1; 0.0<=x<=0.9]
number
0.1
The number of mismatches allowed (as a fraction)
number
0.1
The minimum length of the barcode that must overlap when matching
integer
A 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)
string
The 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’
integer
60
The number of mismatches allowed when collapsing (adjacency)
integer
2
Discard molecules with with a count (reads) lower than this value
integer
2
Use counts when collapsing (the difference in counts between two molecules must be more than double in order to be collapsed)
boolean
Activate the multiplet recovery using leiden community detection
boolean
true
Number of iterations for the leiden algorithm, high values will decrease the variance of the results but increase the runtime [default: 10; 1<=x<=100]
integer
10
Discard edges (pixels) with a count (reads) lower than this, use 1 to disable
integer
2
The minimum size (pixels) a component/cell can have (disabled by default)
integer
The maximum size (pixels) a component/cell can have (disabled by default)
integer
Enable 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)
string
Enable aggregate calling, information on potential aggregates will be added to the output data
boolean
true
Skip analysis step
boolean
Compute polarization scores matrix (clusters by markers)
boolean
true
Compute colocalization scores (marker by marker) for each component
boolean
true
Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores
boolean
Which approach to use to normalize the antibody counts.
string
Transform the antibody counts to 0-1 (binarize) when computing polarization
boolean
Select the type of transformation to use on the node by antibody counts matrix when computing colocalization
string
Select the size of the neighborhood to use when computing colocalization metrics on each component
integer
1
Set the number of permutations use to compute the empirical p-value for the colocalization score
integer
50
The minimum number of counts in a region for it to be considered valid for computing colocalization
integer
5
Skip report generation
boolean
Global configuration options specific to nf-core/pixelator.
Override the container image reference to use for all steps using the pixelator
command.
string
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean