Explore Workflows

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

Graph Name Retrieved From View
workflow graph somatic_exome: exome alignment and somatic variant detection

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 9f3b9e7b74d5a904b12674dfd1300b56a48c3d33
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph SSU-from-tablehits.cwl

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph kmer_gc_extract_wnode

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

Path: task_types/tt_kmer_gc_extract_wnode.cwl

Branch/Commit ID: 33414c888997d558bdcb558ca33c3a728a3e6143
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph 04-quantification-pe-unstranded.cwl

RNA-seq 04 quantification

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/04-quantification-pe-unstranded.cwl

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 70e530b65b33301032b7510095d89e497bf5e34e
workflow graph 01-qc-pe.cwl

ChIP-seq 01 QC - reads: PE

 https://github.com/Duke-GCB/GGR-cwl.git

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

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
workflow graph wf_full_IDR_pipeline_1input_sample.cwl

This workflow essentially restructures the inputs before sending to wf_full_IDR_pipeline_1input.cwl

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_full_IDR_pipeline_1input_sample.cwl

Branch/Commit ID: aedc0a14d4ba109ee65678a3201a52c5bb6ad473