Explore Workflows

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Graph Name Retrieved From View
workflow graph Cellranger aggr - aggregates data from multiple Cellranger runs

Devel version of Single-Cell Cell Ranger Aggregate ================================================== Workflow calls \"cellranger aggr\" command to combine output files from \"cellranger count\" (the molecule_info.h5 file from each run) into a single feature-barcode matrix containing all the data. When combining multiple GEM wells, the barcode sequences for each channel are distinguished by a GEM well suffix appended to the barcode sequence. Each GEM well is a physically distinct set of GEM partitions, but draws barcode sequences randomly from the pool of valid barcodes, known as the barcode whitelist. To keep the barcodes unique when aggregating multiple libraries, we append a small integer identifying the GEM well to the barcode nucleotide sequence, and use that nucleotide sequence plus ID as the unique identifier in the feature-barcode matrix. For example, AGACCATTGAGACTTA-1 and AGACCATTGAGACTTA-2 are distinct cell barcodes from different GEM wells, despite having the same barcode nucleotide sequence. This number, which tells us which GEM well this barcode sequence came from, is called the GEM well suffix. The numbering of the GEM wells will reflect the order that the GEM wells were provided in the \"molecule_info_h5\" and \"gem_well_labels\" inputs. When combining data from multiple GEM wells, the \"cellranger aggr\" pipeline automatically equalizes the average read depth per cell between groups before merging. This approach avoids artifacts that may be introduced due to differences in sequencing depth. It is possible to turn off normalization or change the way normalization is done through the \"normalization_mode\" input. The \"none\" value may be appropriate if you want to maximize sensitivity and plan to deal with depth normalization in a downstream step.

https://github.com/datirium/workflows.git

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph rnaseq-star-rsem-pe.cwl

https://github.com/pitagora-network/dat2-cwl.git

Path: workflow/rna-seq/rnaseq-star-rsem-pe/rnaseq-star-rsem-pe.cwl

Branch/Commit ID: 0cd20e1be620ae0817a1aa4286d73b78c89809f0
workflow graph assm_assm_blastn_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 90a321ecf2d049330bcf0657cc4d764d2c3f42dd
workflow graph blastp_wnode_struct

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: 861d9baa067af98d794ba0ed4e43aa42e37d8a24
workflow graph workflow_simple.cwl

https://github.com/FarahZKhan/scalability-reproducibility-chapter.git

Path: CWL/workflow_simple.cwl

Branch/Commit ID: 639b2bd5bed4c530a1c2b79d0789c43539dfc2c2
workflow graph taxonomy_check_16S

https://github.com/ncbi/pgap.git

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 90a321ecf2d049330bcf0657cc4d764d2c3f42dd
workflow graph example_workflow.cwl

https://github.com/Aeolic/example-workflow.git

Path: example_workflow.cwl

Branch/Commit ID: 2471aac06dafdeaa606b02cc7a83a924036a061b
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph kmer_build_tree

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 4b73bfeb967ee9f57a0410276f7c39e784f0846f
workflow graph Tumor-Only Detect Variants workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c