Explore Workflows

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Graph Name Retrieved From View
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0
workflow graph bam to trimmed fastqs

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph Downsample and HaplotypeCaller

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

Path: definitions/pipelines/downsample_and_recall.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph chipseq-header.cwl

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

Path: metadata/chipseq-header.cwl

Branch/Commit ID: a409db2289b86779897ff19003bd351701a81c50
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: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 02816f0d66e36c8eeba02d211cc90e36bf1c9df5
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: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_download/workflow.cwl

Branch/Commit ID: 7198756b4b1519d102178042924671bd677e9b17