Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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tt_univec_wnode.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_univec_wnode.cwl Branch/Commit ID: 0d9e6bb52eac0c209af3977aa779e39aaa432458 |
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Chipseq alignment with qc and creating homer tag directory
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/chipseq.cwl Branch/Commit ID: f77a920bcc73f6cfdb091eed75a149d02cd8a263 |
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exome alignment and tumor-only variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/exome.cwl Branch/Commit ID: 5c49c5a53259d4c88a02750f1a16a3c02d711115 |
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Bisulfite alignment and QC
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/bisulfite.cwl Branch/Commit ID: f21b6c6f70f01d0fe08193684060161107f0bf59 |
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kmer_ref_compare_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: f5a467a21b8f69aef5666fb7bbf35efd98c0cbea |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
https://github.com/Barski-lab/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: d80d4f126eb60579dc3c3faf90996acc802155f2 |
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kmer_top_n_extract
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n_extract.cwl Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d |
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Single-Cell ATAC-Seq Filtering Analysis
Single-Cell ATAC-Seq Filtering Analysis Removes low-quality cells from the outputs of either the “Cell Ranger Count (ATAC)” or “Cell Ranger Aggregate (ATAC)” pipeline. The results of this workflow are used in the “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipeline. |
https://github.com/datirium/workflows.git
Path: workflows/sc-atac-filter.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895 |
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exome alignment and somatic variant detection for cle purpose
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/cle_somatic_exome.cwl Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28 |
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kmer_top_n_extract
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n_extract.cwl Branch/Commit ID: 55e85a6c1a3d3ae2b47e9ae5363132a12824b1d9 |
