Explore Workflows

\" plant2human main workflow: compare structural similarity and sequence similarity Compare distantly related species, such as plants and humans, using measures of structural similarity and sequence similarity. This workflow will contribute to the discovery of protein-coding genes with features that are “sequence dissimilar but structurally similar”. \"

https://github.com/yonesora56/plant2human.git

Path: Workflow/plant2human.cwl

Branch/Commit ID: 11b46d8d8c0db462edbd2657fc62cf31bc93ecee

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: de847468843203ce92b6d19323c5fe77dc488e34

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

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

Path: tests/wf/revsort_step_bad_schema.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46

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

Path: testdata/step-valuefrom2-wf_v1_1.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0

Validation by expert review (external instrument expert or member of the simulation team).

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

Path: workflows/ValidateParameterByExpert.cwl

Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 7e875f77b615b4f7ebfb23a1da30eb216cc52919

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

Path: testdata/scatter-wf3_v1_2.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0

Packed ID: main

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: 69643d8c15f5357a320aa7e2f6adb2e71302fd20

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

Path: testdata/step-valuefrom2-wf_v1_0.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0