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: a839eb6390974089e1a558c49fc07b4c66c50767
workflow graph QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

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

Path: workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl

Branch/Commit ID: 9d5cbdd3ea0bb417518115d8092584254598a440
workflow graph qsm_pipeline_v1.cwl

https://github.com/MGuevaraO/qsm_pipeline.git

Path: qsm_pipeline_v1.cwl

Branch/Commit ID: 882e36d61371650b06fe1a839a84c488ccdcf77f
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 441b85003fdc10cf4cbf333d89acb4d23b0fef32
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1
workflow graph workflow_mock_ngtax.cwl

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_mock_ngtax.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 441b85003fdc10cf4cbf333d89acb4d23b0fef32
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: d746755df4077476b662271a5d24c4220774a7ee
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 449f87c8365637e803ba66f83367e96f98c88f5c
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b