Explore Workflows

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

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl

Branch/Commit ID: b62c7bfcf5eb7ac3c1ed06879200fdf5db947e4b

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a

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: 10ce6e113f749c7bd725e426445220c3bdc5ddf1

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/trick_revsort.cwl

Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 8cc9b995bca666c54c673a5eb8d9b8c6f8e84490

https://github.com/CRI-iAtlas/iatlas-workflows.git

Path: Kallisto/workflow/kallisto_scatter_synapse_paired_end_workflow.cwl

Branch/Commit ID: 3acab4d22ff0f9657dc8c5685799898a2fc2fd25

Single-cell Differential Expression =================================== Runs differential expression analysis for a subset of cells between two selected conditions.

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

Path: workflows/sc_diff_expr.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1