Components

An overview of the workflows and modules in OpenPipelines

Workflows

Name Namespace Description
Workflows  
BD Rhapsody Ingestion A generic pipeline for running BD Rhapsody WTA or Targeted mapping, with support for AbSeq, VDJ and/or SMK.
Bbknn leiden Multiomics/integration Run bbknn followed by leiden clustering and run umap on the result.
Cell Ranger mapping Ingestion A pipeline for running Cell Ranger mapping.
Cell Ranger multi Ingestion A pipeline for running Cell Ranger multi.
Cell Ranger post-processing Ingestion Post-processing Cell Ranger datasets.
Conversion Ingestion A pipeline to convert different file formats to .h5mu.
Demux Ingestion A generic pipeline for running bcl2fastq, bcl-convert or Cell Ranger mkfastq.
Full pipeline Multiomics A pipeline to analyse multiple multiomics samples.
Harmony leiden Integration/common Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.
Harmony leiden Multiomics/integration Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.
Initialize integration Integration/initialize integration Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.
Initialize integration Multiomics/integration Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.
Integration Multiomics A pipeline for demultiplexing multimodal multi-sample RNA transcriptomics data.
Leiden scvi Multiomics/integration Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result.
Make reference Ingestion Build a transcriptomics reference into one of many formats
Multisample Multiomics This workflow serves as an entrypoint into the ‘full_pipeline’ in order to re-run the multisample processing and the integration setup.
Prot multisample Multiomics Processing unimodal multi-sample ADT data.
Prot singlesample Multiomics Processing unimodal single-sample CITE-seq data.
Rna multisample Multiomics Processing unimodal multi-sample RNA transcriptomics data.
Rna singlesample Multiomics Processing unimodal single-sample RNA transcriptomics data.
Scanorama leiden Integration/scanorama leiden Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result.
Scanorama leiden Multiomics/integration Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result.
Scvi Integration/scvi Run scvi integration followed by neighbour calculations and run umap on the result.
Totalvi leiden Multiomics/integration Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result.
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Modules

Name Namespace Description
Modules  
Add id Metadata Add id of .obs.
BD Rhapsody Mapping A wrapper for the BD Rhapsody Analysis CWL v1.10.1 pipeline
Bbknn Neighbors BBKNN network generation
Bcl convert Demux Convert bcl files to fastq files using bcl-convert.
Bcl2fastq Demux Convert bcl files to fastq files using bcl2fastq
Build bdrhap reference Reference Compile a reference into a STAR index compatible with the BD Rhapsody pipeline.
Build cellranger reference Reference Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files.
Calculate qc metrics Qc Add basic quality control metrics to an .h5mu file.
Cellbender remove background Correction Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.
Cellbender remove background v0 2 Correction Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.
Cellranger count Mapping Align fastq files using Cell Ranger count.
Cellranger count split Mapping Split 10x Cell Ranger output directory into separate output fields.
Cellranger mkfastq Demux Demultiplex raw sequencing data
Cellranger multi Mapping Align fastq files using Cell Ranger multi.
Cellxgene census Query Query CellxGene Census or user-specified TileDBSoma object, and eventually fetch cell and gene metadata or/and expression counts.
Clr Transform Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017)
Compress h5mu Compression Compress a MuData file.
Concat Dataflow Concatenates several uni-modal samples in .h5mu files into a single file
Delete layer Transform Delete an anndata layer from one or more modalities
Do filter Filter Remove observations and variables based on specified .obs and .var columns
Download file Download Download a file
Fastqc Qc Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Filter 10xh5 Process 10xh5 Filter a 10x h5 dataset
Filter with counts Filter Filter scRNA-seq data based on the primary QC metrics.
Filter with hvg Filter Annotate highly variable genes [Satija15] [Zheng17] [Stuart19].
Filter with scrublet Filter Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019).
Find neighbors Neighbors Compute a neighborhood graph of observations [McInnes18].
From 10xh5 to h5mu Convert Converts a 10x h5 into an h5mu file
From 10xmtx to h5mu Convert Converts a 10x mtx into an h5mu file
From bd to 10x molecular barcode tags Convert Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB)
From bdrhap to h5mu Convert Convert the output of a BD Rhapsody WTA pipeline to a MuData h5 file
From cellranger multi to h5mu Convert Converts the output from cellranger multi to a single .h5mu file.
From h5ad to h5mu Convert Converts a single layer h5ad file into a single MuData object
From h5mu to h5ad Convert Converts a h5mu file into a h5ad file
Harmonypy Integrate Performs Harmony integration based as described in https://github.com/immunogenomics/harmony.
Htseq count Mapping Quantify gene expression for subsequent testing for differential expression.
Htseq count to h5mu Mapping Convert the htseq table to a h5mu
Join csv Metadata Join a csv containing metadata to the .obs or .var field of a mudata file.
Join uns to obs Metadata Join a data frame of length 1 (1 row index value) in .uns containing metadata to the .obs of a mudata file.
Knn Labels transfer Performs label transfer from reference to query using KNN classifier
Leiden Cluster Cluster cells using the Leiden algorithm [Traag18] implemented in the Scanpy framework [Wolf18].
Lianapy Interpret Performs LIANA integration based as described in https://github.com/saezlab/liana-py
Log1p Transform Logarithmize the data matrix.
Make params Files Looks for files in a directory and turn it in a params file.
Make reference Reference Preprocess and build a transcriptome reference.
Merge Dataflow Combine one or more single-modality .h5mu files together into one .h5mu file
Mermaid Report Generates a network from mermaid code
Move obsm to obs Metadata Move a matrix from .obsm to .obs.
Multi star Mapping Align fastq files using STAR.
Multi star to h5mu Mapping Convert the output of multi_star to a h5mu
Multiqc Qc MultiQC aggregates results from bioinformatics analyses across many samples into a single report.
Normalize total Transform Normalize counts per cell.
Pca Dimred Computes PCA coordinates, loadings and variance decomposition.
Popv Annotate Performs popular major vote cell typing on single cell sequence data using multiple algorithms.
Publish Transfer Publish an artifact and optionally rename with parameters
Regress out Transform Regress out (mostly) unwanted sources of variation.
Remove modality Filter Remove a modality from a .h5mu file
Samtools sort Mapping Sort and (optionally) index alignments.
Scale Transform Scale data to unit variance and zero mean
Scanorama Integrate Use Scanorama to integrate different experiments
Scarches Integrate Performs reference mapping with scArches
Scvelo Velocity ID: scvelo
Namespace: velocity
Scvi Integrate Performs scvi integration as done in the human lung cell atlas https://github.com/LungCellAtlas/HLCA
Split modalities Dataflow Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files.
Star align Mapping Align fastq files using STAR.
Star align v273a Mapping Align fastq files using STAR.
Star build reference Mapping Create a reference for STAR from a set of fasta files.
Subset h5mu Filter Create a subset of a mudata file by selecting the first number of observations
Sync test resources Download Synchronise the test resources from s3://openpipelines-data to resources_test
Totalvi Integrate Performs mapping to the reference by totalvi model: https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scarches_scvi_tools.html#Reference-mapping-with-TOTALVI
Umap Dimred UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data.
Velocyto Velocity Runs the velocity analysis on a BAM file, outputting a loom file.
Velocyto to h5mu Convert Convert a velocyto loom file to a h5mu file.
Xgboost Labels transfer Performs label transfer from reference to query using XGBoost classifier
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