Explore Workflows
View already parsed workflows here or click here to add your own
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umi molecular alignment workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405 |
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umi molecular alignment workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6 |
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bam to trimmed fastqs and HISAT alignments
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec |
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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/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df |
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Run pindel on provided region
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6 |
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Run pindel on provided region
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec |
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kfdrc_alignment_pipeline.cwl
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https://github.com/kids-first/kf-alignment-workflow.git
Path: dev/pilot-run/worklflows/kfdrc_alignment_pipeline.cwl Branch/Commit ID: 98f0d136e869f23eca89a4188b257d63f30fc44b |
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foreign_screening
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https://github.com/ncbi/pgap.git
Path: vecscreen/foreign_screening.cwl Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee |
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Merge, annotate, and generate a TSV for SVs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec |
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workflow.cwl
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https://github.com/52North/testbed16-jupyter-notebooks.git
Path: workflow_water_masks/workflow.cwl Branch/Commit ID: d0b826dec8d89052a22783a61d60ff762177d893 |
