Explore Workflows

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

Graph	Name	Retrieved From	View
	Per-chromosome pindel	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pindel_cat.cwl Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806
	GAT - Genomic Association Tester GAT: Genomic Association Tester ============================================== A common question in genomic analysis is whether two sets of genomic intervals overlap significantly. This question arises, for example, in the interpretation of ChIP-Seq or RNA-Seq data. The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation. Gat implemements a sampling algorithm. Given a chromosome (workspace) and segments of interest, for example from a ChIP-Seq experiment, gat creates randomized version of the segments of interest falling into the workspace. These sampled segments are then compared to existing genomic annotations. The sampling method is conceptually simple. Randomized samples of the segments of interest are created in a two-step procedure. Firstly, a segment size is selected from to same size distribution as the original segments of interest. Secondly, a random position is assigned to the segment. The sampling stops when exactly the same number of nucleotides have been sampled. To improve the speed of sampling, segment overlap is not resolved until the very end of the sampling procedure. Conflicts are then resolved by randomly removing and re-sampling segments until a covering set has been achieved. Because the size of randomized segments is derived from the observed segment size distribution of the segments of interest, the actual segment sizes in the sampled segments are usually not exactly identical to the ones in the segments of interest. This is in contrast to a sampling method that permutes segment positions within the workspace.	https://github.com/datirium/workflows.git Path: workflows/gat-run.cwl Branch/Commit ID: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e
	mut2.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mut2.cwl Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
	env-wf2.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/env-wf2.cwl Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
	Build STAR indices Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_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/star-index.cwl Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
	AcceptParameterFailure validation or review of parameter updates failed. Action required and feedback to be provided.	https://github.com/gammasim/workflows.git Path: workflows/AcceptParameterFailure.cwl Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
	trim-rnaseq-pe.cwl Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
	Quality assessment, amplicon classification and functional prediction Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax	https://git.wur.nl/unlock/cwl.git Path: cwl/workflows/workflow_ngtax_picrust2.cwl Branch/Commit ID: 2242521957bb07fc589d6bb07046f6a166bc975a
	animal-genome-assembly.with_canu.cwl Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano). This workflow contains assembly step by canu which may take a few weeks to complete. Be careful to run!	https://github.com/pitagora-network/DAT2-cwl.git Path: workflow/animal-genome-assembly/animal-genome-assembly.with_canu.cwl Branch/Commit ID: b63171820f546def8c26f558182912a71af88b48