Explore Workflows

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 ============================================== 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

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: f02557902989c749c9c2187c7045e340e2d76bfc

https://github.com/pvanheus/lukasa.git

Path: make_search_pair_workflow.cwl

Branch/Commit ID: 0ed49ec431ed0fdb481231b47c19d939d29c58c6

Devel version of Single-Cell Cell Ranger Reanalyze ================================================== Workflow calls \"cellranger aggr\" command to rerun secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering and visualization) using different parameter settings. As an input we use filtered feature-barcode matrices in HDF5 format from cellranger count or aggr experiments. Note, we don't pass aggregation_metadata from the upstream cellranger aggr step. Need to address this issue when needed.

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: e0a30aa1ad516dd2ec0e9ce006428964b840daf4

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-qc-paired.cwl

Branch/Commit ID: d4e5e533ee6dc93bfaf1c4bbb2ab40812a8f4792

The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_full_IDR_pipeline_2inputs_scatter.cwl

Branch/Commit ID: 18933d4d4b00e97a8a0d155abbebad1fdbc254aa

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

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 0b6e8fd8ead7644cf5398395b76af5cf4011686f

https://github.com/stain/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-wf.cwl

Branch/Commit ID: b1e88a8c2f6f07d236193d3e89dc2d724700780a

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-01-preprocessing.cwl

Branch/Commit ID: e82f3a71183048dd6700ec6725ee526ac1a95238