Explore Workflows

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Graph Name Retrieved From View
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
workflow graph Gathered Downsample and HaplotypeCaller

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

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 742dbafb5fb103d8578f48a0576c14dd8dae3b2a
workflow graph 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: 799575ce58746813f066a665adeacdda252d8cab
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 001fab592188cb525afa1c4db6226b833faec106
workflow graph SPRM pipeline

https://github.com/hubmapconsortium/sprm.git

Path: pipeline.cwl

Branch/Commit ID: 4ec0294484610b3f7811bc4f64773ac3833b8b8a
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/alignment_exome_mouse.cwl

Branch/Commit ID: c625e05eefb1754353c1bdfa46c01dc61e6233dd
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
workflow graph steplevel-resreq.cwl

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

Path: v1.0/v1.0/steplevel-resreq.cwl

Branch/Commit ID: e67f19d8a713759d761ecad050966d1eb043b85c