Explore Workflows

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

Graph	Name	Retrieved From	View
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: 45d134ce3d436c53637a2d83755e9b4613267e9f
	bam to trimmed fastqs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325
	cache_asnb_entries	https://github.com/ncbi-gpipe/pgap.git Path: task_types/tt_cache_asnb_entries.cwl Branch/Commit ID: 70e530b65b33301032b7510095d89e497bf5e34e
	exome alignment and germline variant detection	https://github.com/litd/analysis-workflows.git Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 336f7d1af649f42543baa6be2594cd872919b5b5
	THOR - differential peak calling of ChIP-seq signals with replicates What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.	https://github.com/datirium/workflows.git Path: workflows/rgt-thor.cwl Branch/Commit ID: 2f0db4b3c515f91c5cfda19c78cf90d339390986
	Hello World Puts a message into a file using echo	https://github.com/markrobbo/workflows.git Path: workflows/hello/hello.cwl Branch/Commit ID: 0ae2468ab2ba0b9a196c2aa89b580555750bf0f6 Packed ID: main
	tt_kmer_top_n.cwl	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: 75ea689c0a8c9902b4598b453455857cb08e885a
	MAnorm PE - quantitative comparison of ChIP-Seq paired-end 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 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: 2c486543c335bb99b245dfe7e2f033f535efb9cf
	Cell Ranger Build Reference Indices Devel version of Cell Ranger Build Reference Indices pipeline =============================================================	https://github.com/datirium/workflows.git Path: workflows/cellranger-mkref.cwl Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422
	WGS QC workflow nonhuman	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_wgs_nonhuman.cwl Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c