Explore Workflows

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/record-in-secondaryFiles-wf.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042

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

Path: definitions/pipelines/gathered_somatic_exome.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines19-wf.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

https://github.com/common-workflow-library/bio-cwl-tools.git

Path: bwa/BWA-Mem2-single.cwl

Branch/Commit ID: 810495363e06f80529633389ec25f8bb6b961844

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

Path: testdata/step_valuefrom5_wf_v1_1.cwl

Branch/Commit ID: c1875d54dedc41b1d2fa08634dcf1caa8f1bc631

What is MAnorm? -------------- MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications and you can use it for: * Normalization of two ChIP-seq samples * Quantitative comparison (differential analysis) of two ChIP-seq samples * Evaluating the overlap enrichment of the protein binding sites(peaks) * Elucidating underlying mechanisms of cell-type specific gene regulation How MAnorm works? ---------------- MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should exhibit similar global binding intensities across samples. The observed differences on common peaks are presumed to reflect the scaling relationship of ChIP-Seq signals between two samples, which can be applied to all peaks. What do the inputs mean? ---------------- ### General **Experiment short name/Alias** * short name for you experiment to identify among the others **ChIP-Seq SE sample 1** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 1 **ChIP-Seq SE sample 2** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 2 **Genome** * Reference genome to be used for gene assigning ### Advanced **Reads shift size for sample 1** * This value is used to shift reads towards 3' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **Reads shift size for sample 2** * This value is used to shift reads towards 5' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **M-value (log2-ratio) cutoff** * Absolute M-value (log2-ratio) cutoff to define biased (differential binding) peaks. Default: 1.0 **P-value cutoff** * P-value cutoff to define biased peaks. Default: 0.01 **Window size** * Window size to count reads and calculate read densities. 2000 is recommended for sharp histone marks like H3K4me3 and H3K27ac, and 1000 for TFs or DNase-seq. Default: 2000

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

Path: workflows/manorm-se.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: gatk4-mutect2-tumor-only-cwl/gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl

Branch/Commit ID: cc7d31c9b8e5a0d0be41203513007df2cb341f73

https://github.com/bcbio/bcbio_validation_workflows.git

Path: SGDP-recall-CGC/SGDP-recall-cgc/main-SGDP-recall.cwl

Branch/Commit ID: 9606af30d5f047745a1cd7ec1a59d65508ed256e

Single-Cell ATAC-Seq Genome Coverage Generates genome coverage tracks from chromatin accessibility data of selected cells

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

Path: workflows/sc-atac-coverage.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3