Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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Exome QC workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_exome.cwl Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54 |
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1st-workflow.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/1st-workflow.cwl Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda |
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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: b8000c793d6e7ce4d690406c4f914c5c62acd51f |
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heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
https://github.com/Barski-lab/workflows.git
Path: tools/heatmap-prepare.cwl Branch/Commit ID: d09a44ebc8d092ffd8370a324c9e84b37a593d38 |
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Single-cell Differential Expression
Single-cell Differential Expression =================================== Runs differential expression analysis for a subset of cells between two selected conditions. |
https://github.com/datirium/workflows.git
Path: workflows/sc_diff_expr.cwl Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5 |
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Add snv and indel bam-readcount files to a vcf
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/vcf_readcount_annotator.cwl Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f |
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Tumor-Only Detect Variants workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/tumor_only_detect_variants.cwl Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f |
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Immunotherapy Workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/immuno.cwl Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f |
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chip-seq-alignment.cwl
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https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/ChIP-Seq/chip-seq-alignment.cwl Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098 |
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Whole genome alignment and somatic variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_wgs.cwl Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f |
