Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: 9a8e654a91ea5d26e8452dd1cecf3faf22b7a12e

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 5c4125344b1b9125ad04d7e768ecc99901570a7a

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: 64f7fe4438898218fd83133efa25251078f5b27e

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

Path: v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl

Branch/Commit ID: 4d06b9efd26c5813c13684ebcc95547bb75ddfcc

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/AddBamStatsSomatic_v0_1_0.cwl

Branch/Commit ID: c1aeec7b68acdd1eab3f1d1bd75d768e31abd6d2

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 5c4125344b1b9125ad04d7e768ecc99901570a7a

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: 74647cc0f1abac4ee22950cfa89c44cf2ca3cffd

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: a539d600357a48a558daf43fc41a89aae79f9e86

Devel version of AltAnalyze Iterative Clustering and Guide-gene Selection =========================================================================

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: 64f7fe4438898218fd83133efa25251078f5b27e

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: 74647cc0f1abac4ee22950cfa89c44cf2ca3cffd