Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 87faba2fff8007ecc95160729b1c7cd0376e46f2
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
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: 09267e79fd867aa68a219c69e6db7d8e2e877be2
workflow graph word-mapping-test-files-wf.cwl#word-mapping-wf.cwl

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/word-mapping-test-files-wf.cwl

Branch/Commit ID: bfd504ae910fbf7a3492f53430a1c9f3c3c97470

Packed ID: word-mapping-wf.cwl
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325
workflow graph Alignment without BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325
workflow graph CLE gold vcf evaluation workflow

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

Path: definitions/subworkflows/vcf_eval_cle_gold.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71