Explore Workflows

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/basic_sep.cwl

Branch/Commit ID: 81d4bdaecebaa843903b40834cb15e350aa047e8

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines11-null-step-wf-noET.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050

FASTQ Download Downloads FASTQ files from the provided SRR identifiers

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

Path: workflows/fastq-download.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

Workflow to convert a maf file into a vcf.gz with .tbi index

https://github.com/mskcc/pluto-cwl.git

Path: cwl/maf2vcf_gz_workflow.cwl

Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4

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

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: a8d8d00fd1e4274e1bc16001937db5aae46b0b0d

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5

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

Path: cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl

Branch/Commit ID: e8b3565a008d95859fc44227987a54e6a53a8c29

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/dnaseq/etl_http.cwl

Branch/Commit ID: f34d3963b33e0a379338cb3cb75b0016f012bf2c

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 PE sample 1** * previously analyzed ChIP-Seq paired-end experiment to be used as Sample 1 **ChIP-Seq PE sample 2** * previously analyzed ChIP-Seq paired-end 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-pe.cwl

Branch/Commit ID: b5e16e359007150647b14dc6e038f4eb8dccda79