Explore Workflows

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

Graph	Name	Retrieved From	View
	exome alignment and somatic variant detection for cle purpose	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome_cle.cwl Branch/Commit ID: 0b6e8fd8ead7644cf5398395b76af5cf4011686f
	env-wf1.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
	Alignment without BQSR	https://github.com/tmooney/cancer-genomics-workflow.git Path: definitions/subworkflows/sequence_to_bqsr_mouse.cwl Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8
	Filter single sample sv vcf from paired read callers(Manta/Smoove)	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
	alignment for nonhuman with qc	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_wgs_nonhuman.cwl Branch/Commit ID: 04d21c33a5f2950e86db285fa0a32a6659198d8a
	Chipseq alignment with qc and creating homer tag directory	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/chipseq.cwl Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
	conflict-wf.cwl#collision	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl Branch/Commit ID: 4df56e95e6fceab69e677b539f3532cbf5946197 Packed ID: collision
	GAT - Genomic Association Tester GAT: Genomic Association Tester ============================================== A common question in genomic analysis is whether two sets of genomic intervals overlap significantly. This question arises, for example, in the interpretation of ChIP-Seq or RNA-Seq data. The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation. Gat implemements a sampling algorithm. Given a chromosome (workspace) and segments of interest, for example from a ChIP-Seq experiment, gat creates randomized version of the segments of interest falling into the workspace. These sampled segments are then compared to existing genomic annotations. The sampling method is conceptually simple. Randomized samples of the segments of interest are created in a two-step procedure. Firstly, a segment size is selected from to same size distribution as the original segments of interest. Secondly, a random position is assigned to the segment. The sampling stops when exactly the same number of nucleotides have been sampled. To improve the speed of sampling, segment overlap is not resolved until the very end of the sampling procedure. Conflicts are then resolved by randomly removing and re-sampling segments until a covering set has been achieved. Because the size of randomized segments is derived from the observed segment size distribution of the segments of interest, the actual segment sizes in the sampled segments are usually not exactly identical to the ones in the segments of interest. This is in contrast to a sampling method that permutes segment positions within the workspace.	https://github.com/datirium/workflows.git Path: workflows/gat-run.cwl Branch/Commit ID: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
	iwdr_with_nested_dirs.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/iwdr_with_nested_dirs.cwl Branch/Commit ID: f02557902989c749c9c2187c7045e340e2d76bfc
	make_search_pair_workflow.cwl	https://github.com/pvanheus/lukasa.git Path: make_search_pair_workflow.cwl Branch/Commit ID: 0ed49ec431ed0fdb481231b47c19d939d29c58c6