Versioning
The nf-core/pixelator pipeline is versioned separately from the pixelator command-line tool.
Each release of nf-core/pixelator should use a specific version of pixelator.
Sometimes the version of pixelator will be different than the one used by the pipeline.
Here we explain how to use a different version of nf-core/pixelator among the released ones. And how to use features under development.
Selecting the pipeline version
Nextflow pipelines can easily switch between pipeline versions using the underlying Git version control system. Selecting versions depends on how you run the pipeline.
The easiest option is to use nextflow to fetch and manage pipeline versions.
Updating nf-core/pixelator
nextflow pull nf-core/pixelator
When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline.
By ensuing you run the latest nf-core/pixelator version, you make sure that you also run the latest pixelator version as we will keep them version compatible.
Reproducibility
It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
First, go to the nf-core/pixelator releases page
and find the latest version number - numeric only (eg. 1.3.1).
Then specify this when running the pipeline with -r (one hyphen) - eg. -r 1.3.1.
This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
Using the development version
You will need to have git installed to allow nextflow clone and update our nf-core/pixelator development version. Nextflow allows to launch the execution of our development pipeline hosted on the Pixelgen Technologies GitHub repository.
nextflow run PixelgenTechnologies/nf-core-pixelator -r pixelator-next --help
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/PixelgenTechnologies/nf-core-pixelator` [drunk_thompson] DSL2 - revision: 2f3b96085c [pixelator-next]
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`._,._,'
nf-core/pixelator v1.0.3-g2f3b960
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Typical pipeline command:
nextflow run nf-core/pixelator --input samplesheet.csv --output results -profile docker
Input/output options
--input [string] Path to comma-separated file containing information about the samples in the experiment.
--input_basedir [string] Path to a local or remote directory that is the "current working directory" for relative paths defined in the
input samplesheet
--outdir [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud
infrastructure. [default: ./results]
--email [string] Email address for completion summary.
QC/Filtering/Trimming options
--trim_front [integer] Trim N bases from the front of the reads [default: 0]
--trim_tail [integer] Trim N bases from the tail of the reads [default: 0]
--max_length [integer] The maximum length of a read
--min_length [integer] The minimum length (bases) of a read
--max_n_bases [integer] The maximum number of Ns allowed in a read [default: 0]
--avg_qual [integer] Minimum avg. quality a read must have (0 will disable the filter) [default: 20]
--dedup [boolean] Remove duplicated reads (exact same sequence)
--remove_polyg [boolean] Remove PolyG sequences (length of 10 or more)
Adapter QC Options
--adapterqc_mismatches [number] The number of mismatches allowed (in percentage) [default: 0.1; 0.0<=x<=0.9] [default: 0.1]
Demux options
--demux_mismatches [number] The number of mismatches allowed (as a fraction) [default: 0.1]
--demux_min_length [integer] The minimum length of the barcode that must overlap when matching
Collapse options
--markers_ignore [string] A list of comma separated antibodies to discard
--algorithm [string] The algorithm to use for collapsing (adjacency will perform error correction using the number of mismatches
given) (accepted: adjacency, unique) [default: adjacency]
--collapse_mismatches [integer] The number of mismatches allowed when collapsing (adjacency) [default: 2]
--collapse_min_count [integer] Discard molecules with with a count (reads) lower than this value [default: 2]
--collapse_use_counts [boolean] Use counts when collapsing (the difference in counts between two molecules must be more than double in order to
be collapsed)
Options for pixelator graph command.
--multiplet_recovery [boolean] Activate the multiplet recovery using leiden community detection [default: true]
Options for pixelator annotate command.
--min_size [integer] The minimum size (pixels) a component/cell can have (disabled by default)
--max_size [integer] The maximum size (pixels) a component/cell can have (disabled by default)
--dynamic_filter [string] 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) (accepted: both, min, max)
[default: min]
--aggregate_calling [boolean] Enable aggregate calling, information on potential aggregates will be added to the output data [default:
true]
Options for pixelator analysis command.
--skip_analysis [boolean] Skip analysis step
--compute_polarization [boolean] Compute polarization scores matrix (clusters by markers) [default: true]
--compute_colocalization [boolean] Compute colocalization scores (marker by marker) for each component [default: true]
--use_full_bipartite [boolean] Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and
colocalization scores
--polarization_normalization [string] Which approach to use to normalize the antibody counts. (accepted: raw, clr, denoise) [default: clr]
--polarization_binarization [boolean] Transform the antibody counts to 0-1 (binarize) when computing polarization
--colocalization_transformation [string] Select the type of transformation to use on the node by antibody counts matrix when computing colocalization
(accepted: raw, clr, log1p, relative) [default: log1p]
--colocalization_neighbourhood_size [integer] Select the size of the neighborhood to use when computing colocalization metrics on each component [default:
1]
--colocalization_n_permutations [integer] Set the number of permutations use to compute the empirical p-value for the colocalization score [default:
50]
--colocalization_min_region_count [integer] The minimum number of counts in a region for it to be considered valid for computing colocalization
[default: 5]
Options for pixelator report command.
--skip_report [boolean] Skip report generation
Global options
--pixelator_container [string] Override the container image reference to use for all steps using the `pixelator` command.
!! Hiding 24 params, use --validationShowHiddenParams to show them !!
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If you use nf-core/pixelator for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.10015112
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/pixelator/blob/master/CITATIONS.md
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If you already have checked out the pipeline once, you can update it with nextflow.
nextflow pull PixelgenTechnologies/nf-core-pixelator
Then, you can run our latest (and under development) version with:
nextflow run PixelgenTechnologies/nf-core-pixelator -r pixelator-next -profile test,docker --outdir results
You can use many parameters with the nf-core/pixelator pipeline.
Overriding pixelator containers
The pipeline is using a pre-configured version of pixelator in all its steps. The nf-core/pixelator pipeline offers a way to override this setting.
It is not recommended to modify the version of pixelator unless it is really needed, for example, to test out a new feature or if you are planning to contribute with code or debug a problem.
Using a version of pixelator different from the default pre-configured can break the pipeline. Use it at your own risk.
--pixelator_container
As most execution profiles will use containers to run the pipeline., the nf-core/pixelator pipeline provides the --pixelator_container parameter to override the container of pixelator without having to write
custom nextflow configuration files.
This flag can be used to override the pixelator container. A container repository URL and a tag must be provided here.
This string will be passed to the container directive of the nextflow modules that use pixelator.
The following example will use the pixelator container version 0.13.1 from Pixelgen Technologies GitHub instead of the
default image available through the BioContainers project on quay.io:
nextflow run nf-core/pixelator --pixelator_container ghcr.io/pixelgentechnologies/pixelator:0.13.1 --help
Modify the following command with your own parameters in order to use the latest development version of pixelator:
nextflow run nf-core/pixelator --pixelator_container ghcr.io/pixelgentechnologies/pixelator:dev <other_cmd_options>