Explore Workflows

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

Graph Name Retrieved From View
workflow graph Peptide and Protein ID using OpenMS tools

Adapted from https://gxy.io/GTN:T00228 1. Florian Christoph Sigloch, Björn Grüning, Peptide and Protein ID using OpenMS tools (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/tutorial.html Online; accessed Thu Jul 13 2023 2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752 3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

https://github.com/SGSSGene/OpenMS.git

Path: workflow/cwl/peptide_and_protein_id/peptide_and_protein_id.cwl

Branch/Commit ID: 5f9367169ac8125ae581b028ff0478698c14f884
workflow graph wgs alignment and tumor-only variant detection

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

Path: definitions/pipelines/wgs.cwl

Branch/Commit ID: 641bdeffd942f5121e19626a094c8633386ad546
workflow graph count-lines11-wf.cwl

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

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

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: add6b7724698694e0e72d972e2e85e1ae4e67902
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f
workflow graph 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: 282762f8bbaea57dd488115745ef798e128bade1
workflow graph env-wf3.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: ec2cf2da6c31ffedf827a0fb213b5204e172f510
workflow graph chipseq-pe.cwl

ChIP-Seq basic analysis workflow for a paired-end experiment.

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

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf
workflow graph js-expr-req-wf.cwl#wf

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

Path: v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9

Packed ID: wf
workflow graph fail-unconnected.cwl

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

Path: v1.0/v1.0/fail-unconnected.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad