Explore Workflows

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_dispatch/2other_species/workflow.cwl

Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f

Workflow for running the facets suite workflow on a single tumor normal pair Includes handling of errors in case execution fails for the sample pair

https://github.com/mskcc/pluto-cwl.git

Path: cwl/facets-suite-workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933

Workflow to run GetBaseCountsMultiSample fillout on a number of bam files with a single maf file

https://github.com/mskcc/pluto-cwl.git

Path: cwl/fillout_workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933

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: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b

Devel version of Cell Ranger Build Reference Indices pipeline =============================================================

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

Path: workflows/cellranger-mkref.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46

https://github.com/athenarc/whole-exome-seq.git

Path: workflows/Whole_Exome-Seq.cwl

Branch/Commit ID: de6ee08d2ff7621c3e07e70881624f342da8b826

https://github.com/arvados/bh20-seq-resource.git

Path: workflows/fastq2fasta/fastq2fasta.cwl

Branch/Commit ID: 2ae71911cd87ce4f2eabdff21e538267b3270d45

**Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning**<br> - Workflow Nanopore Quality - Kraken2 taxonomic classification of FASTQ reads - Flye (de-novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) **When Illumina reads are provided:** - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - Assembly polishing with Pilon<br> - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2 - CheckM - BUSCO - GTDB-Tk **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br>

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_nanopore_assembly.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0

https://github.com/kathy-t/ghapps-single-workflow.git

Path: Dockstore.cwl

Branch/Commit ID: d39c5b5a0939eaa544bb200afe94d75ecddac405