Explore Workflows

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f

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

Path: structuralvariants/workflow.cwl

Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f

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

Path: structuralvariants/subworkflows/bwa_index.cwl

Branch/Commit ID: 7fe278136146cbe6567816f1819f0725afeba021

https://github.com/Gepiro/rCASC_StreamFlow.git

Path: setting/testTimeSIMLR.cwl

Branch/Commit ID: 66b57e54849d71a0acbd17466ee5f833cf041528

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

Path: bacterial_annot/wf_bacterial_annot_pass1.cwl

Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: 89ccbfc53ff3bb6abe2eb90bb7e0091c54c18f5c

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: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620

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

Path: cwl/wf_get_peaks_pe.cwl

Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256

CNV GRIDSS calling

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

Path: structuralvariants/subworkflows/cnv_gridss.cwl

Branch/Commit ID: 7fe278136146cbe6567816f1819f0725afeba021