Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	1st-workflow.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/1st-workflow.cwl Branch/Commit ID: 596aab620489cd2611f4bc1d9a4fc914ddf34514
	Unaligned to aligned BAM	https://github.com/fgomez02/analysis-workflows.git Path: definitions/subworkflows/align.cwl Branch/Commit ID: 9c9e6a6a48eb321804ce772a2c2c12b4f2f32529
	FASTQ to BQSR	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/fastq_to_bqsr.cwl Branch/Commit ID: 3a822294da63b4e19446a285e2fef075e23cf3d0
	Detect DoCM variants	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: 891c996dbd23d8154ec7609a56da3de841ae124c
	ani_top_n	https://github.com/ncbi/pgap.git Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: f18c1dce463509170ee3bf2844d5a3637ff706f5
	umi molecular alignment fastq workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_umi_molecular.cwl Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
	downsample unaligned BAM and align	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: 54846feabbf008c1946db2a86d87252e0edd95b0
	bulk_process.cwl	https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git Path: steps/bulk_process.cwl Branch/Commit ID: 6aad6cf080303e682e5f965f86ddd3c6534ad4a3
	MAnorm SE - quantitative comparison of ChIP-Seq single-read data 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: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e
	Detect Variants workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/detect_variants_mouse.cwl Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a