Explore Workflows

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f

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: 8a92669a566589d80fde9d151054ffc220ed4ddd

Workflow for Metagenomics binning from assembly.<br> Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file Summary - MetaBAT2 (binning) - MaxBin2 (binning) - SemiBin (binning) - DAS Tool (bin merging) - EukRep (eukaryotic classification) - CheckM (bin completeness and contamination) - BUSCO (bin completeness) - GTDB-Tk (bin taxonomic classification) Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default<br><br> **All tool CWL files and other workflows can be found here:**<br> Tools: https://gitlab.com/m-unlock/cwl<br> Workflows: https://gitlab.com/m-unlock/cwl/workflows<br> **How to setup and use an UNLOCK workflow:**<br> https://m-unlock.gitlab.io/docs/setup/setup.html<br>

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_binning.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503

https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git

Path: Assembly/workflow/assembly-wf-virus.cwl

Branch/Commit ID: 9cb4f73c8b490faebcc39fdd6fe37f693a2e5213

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: bccb338be356db83ad178be2aa9634ae86cb5211

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/waltz/waltz_workflow_all_bams.cwl

Branch/Commit ID: 7061957d31023d922501fba61310b2d82de61c15

https://github.com/duke-gcb/bespin-cwl.git

Path: subworkflows/exomeseq-gatk4-03-organizedirectories.cwl

Branch/Commit ID: bbe24d8d7fde2e918583b96805909a2867b749d6

ChIP-seq 01 QC - reads: PE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/01-qc-pe.cwl

Branch/Commit ID: 33385c6a820a9d4d18cff6fc3a533ec8e3c11c6e

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0