Explore Workflows

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

Graph	Name	Retrieved From	View
	cram_to_bam workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cram_to_bam_and_index.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
	Build Bowtie indices Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome	https://github.com/datirium/workflows.git Path: workflows/bowtie-index.cwl Branch/Commit ID: 9850a859de1f42d3d252c50e15701928856fe774
	align_sort_sa	https://github.com/ncbi/pgap.git Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: 02816f0d66e36c8eeba02d211cc90e36bf1c9df5
	Bisulfite alignment and QC	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/bisulfite.cwl Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
	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
	bam to trimmed fastqs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
	Downsample and HaplotypeCaller	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/downsample_and_recall.cwl Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
	mutect parallel workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/mutect.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
	chipseq-header.cwl	https://github.com/datirium/workflows.git Path: metadata/chipseq-header.cwl Branch/Commit ID: a409db2289b86779897ff19003bd351701a81c50
	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