Explore Workflows

https://github.com/YinanWang16/tso500-ctdna-post-processing.git

Path: cwl/workflows/mk_coverage_QC_from_bed.cwl

Branch/Commit ID: 08f855a08ca02b15c8d3540b28bb17b4f85a371a

this is a placeholder for a missing acceptance workflow.

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

Path: workflows/AcceptParameterWorkflowMissing.cwl

Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5

https://github.com/ResearchObject/runcrate.git

Path: cwl/revsortlcase/revsort.cwl

Branch/Commit ID: 376f6b2c6332a4742d4512d6e1fb785a2f8b7285

Filters ChIP/ATAC/cut&run/diffbind peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC/cut&run/diffbind pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

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

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20

Transform array element coordinates into the coordinate system required by the simulation pipeline (i.e., CORSIKA system).

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

Path: workflows/SetArrayElementCoordinates.cwl

Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5

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

Path: testdata/scatter-wf1_v1_2.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0

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

Path: tests/wf/packed_no_main.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46

Packed ID: collision

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

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

Path: workflows/bowtie-index.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20

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: 69643d8c15f5357a320aa7e2f6adb2e71302fd20