nf-core/pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
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|yml|yaml)$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Path to a local or remote directory that is the "current working directory" for relative paths defined in the input samplesheet
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
Save intermediate amplicon reads generated from the raw input reads.
booleanSave intermediate amplicon reads generated from the raw input reads.
booleanThe number of mismatches allowed while anchoring reads using LBS sequences (in percentage of seen LBS length) [default: 0.1; 0.0<=x<=0.5]
numberRemove PolyG sequences (length of 10 or more)
booleanMinimum average quality a read must have. Pass 0 to disable quality filtering.
integer20Trim 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]
number0.1Save intermediate QC read files containing all reads that passed the filters.
booleanSave intermediate QC read files containing all reads that failed the filters.
booleanThe 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
Save intermediate QC read files containing all reads that contain valid antibody barcodes.
booleanSave intermediate QC read files containing all reads that failed the filters.
booleanThe number of mismatches allowed in marker barcodes.
number1The target number of reads in a single file of the partitioned demux output.
string50MThe maximum number of chunks that the demuxed ouput for each umi region will be split into
number8The demux and collapsing strategy to use
stringSave intermediate parquet files containing embeddings of all reads that contain valid antibody barcodes.
booleanSave intermediate FASTQC read files containing all reads that contain valid antibody barcodes.
booleanSave intermediate FASTQC read files containing all reads that do not contain valid antibody barcodes.
booleanA 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
integer2Save an intermediate parquet file containing collapsed read information.
booleanThe algorithm to use for collapsing.
stringThe number of mismatches allowed when collapsing (adjacency)
integer2Save an intermediate parquet file containing collapsed read information.
booleanActivate the multiplet recovery using leiden community detection
booleantrueThe number of times a component can be broken down into smaller components during the multiplet recovery process.
integer5Maximum number of edges between the produced components as a result of a component split operation during the multiplet recovery process.
integer5Discard edges (pixels) with a count (reads) lower than this, use 1 to disable
integer2Save an intermediate CSV file containing the unfiltered graph edge list.
booleanThe 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.
stringFollowing options are available:
- both: estimates both minimum and maximum component size
- min: estimates the minimum component size (or uses {MINIMUM_N_EDGES_CELL_SIZE} edges, whichever is smallest)
- max: estimates the maximum component size.
Note that this cannot be set at the same time as --min-size or --max-size.
Enable aggregate calling, information on potential aggregates will be added to the output data
booleantrueSave the raw_component_metrics.csv file from the annotate stage.
booleanSave the PXL dataset after the annotate stage.
booleanSave the PXL dataset after the graph stage.
booleanActivate the multiplet recovery using leiden community detection
booleantrueNumber of iterations for the leiden algorithm.
number1The resolution parameter for the leiden algorithm at the initial stage.
number1The resolution parameter for the leiden algorithm at the refinement stage.
number0.01Discard edges with a read count below given value. Set to 1 to disable filtering.
number1The minimum component size to consider for refinement
number1000The maximum recursion depth for the refinement algorithm. Set to 1 to disable refinement.
number5The maximum number of edges to remove between components during the initial stage (iteration == 0) of multiplet recovery.
numberThe maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery.
number4The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the initial stage (iteration == 0) of multiplet recovery.
numberThe maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the refinement stage (iteration > 0) of multiplet recovery.
numberThe minimum number of nodes in an potential new components in order for it to be pruned.
number100Components with fewer nodes than this will be filtered from the output data. This is typically not needed. Setting this will disable the automatic size filtering.
numberSkip 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 transformation to use for the antibody counts when calculating polarity scores.
stringraw: use the raw counts.log1p: use the log1p-transformed counts.
Set the number of permutations use to compute the empirical z- and p-values for the polarity score
integer50The minimum number of counts of a marker to calculate the polarity score in the component
integer5Select 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
integer5The minimum number of counts in a component for it to be considered valid for computing colocalization
integer5Save the PXL dataset after the analysis stage.
booleanSave the PXL dataset after the analysis stage.
booleanCompute proximity scores
booleantrueCompute k-core summary tables for each component
booleanNumber of permutations to use when computing the expected proximity scores
integer100Compute the variance explained by the SVD components
booleantrueNumber of pivots to use for the SVD decomposition
integer50Skip layout step
booleanSkip adding marker counts to the layout.
booleanSelect a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: fruchterman_reingold, fruchterman_reingold_3d, kamada_kawai, kamada_kawai_3d, pmds, pmds_3d
stringwpmds_3d(\S+)?(,\S+)*Skip adding marker counts to the layout.
booleanSelect a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: fruchterman_reingold, fruchterman_reingold_3d, kamada_kawai, kamada_kawai_3d, pmds, pmds_3d
stringwpmds_3d(\S+)?(,\S+)*Number of pivots to use for the PMDS layout algorithm. Default: 50. More gives better results, but increases computation time.
integer50The window size used when computing probability weights for the wpmds layout method. Only used when layout algorithm is set to wpmds.
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 guaranteed to work when using different pixelator versions.
Save all intermediate results.
booleanSave all intermediate results for the PNA workflow.
booleantrueParameters 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.
stringLess common options for the pipeline, typically set in a config file.
Display 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.
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.
Boolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/pixelator/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string