Explore Workflows

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

Graph	Name	Retrieved From	View
	Subworkflow that runs cnvkit in single sample mode and returns a vcf file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
	basename-fields-test.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/basename-fields-test.cwl Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd
	kmer_cache_retrieve	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_cache_retrieve.cwl Branch/Commit ID: 68058b108cb5b0b72ebe244c42eefa2747e1d64a
	Unaligned bam to sorted, markduped bam	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/align_sort_markdup.cwl Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2
	kmer_build_tree	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_build_tree.cwl Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53
	Bisulfite QC tools	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bisulfite_qc.cwl Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
	count-lines12-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/count-lines12-wf.cwl Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
	GSEApy - Gene Set Enrichment Analysis in Python GSEAPY: Gene Set Enrichment Analysis in Python ============================================== Gene Set Enrichment Analysis is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA requires as input an expression dataset, which contains expression profiles for multiple samples. While the software supports multiple input file formats for these datasets, the tab-delimited GCT format is the most common. The first column of the GCT file contains feature identifiers (gene ids or symbols in the case of data derived from RNA-Seq experiments). The second column contains a description of the feature; this column is ignored by GSEA and may be filled with “NA”s. Subsequent columns contain the expression values for each feature, with one sample's expression value per column. It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived. The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. Tools such as DESeq2 can be made to produce properly normalized data (normalized counts) which are compatible with GSEA.	https://github.com/datirium/workflows.git Path: workflows/gseapy.cwl Branch/Commit ID: ee66d03be8a7fd61367db40c37a973ff55ece4da
	phase VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/phase_vcf.cwl Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
	default-dir5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-dir5.cwl Branch/Commit ID: bffea7fd5e864c5221c13a815d00d0a2fad178cc