Explore Workflows

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

Graph Name Retrieved From View
workflow graph step-valuefrom3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 42712bca4c3307d87b6b55f525a4c97cb6f7e288
workflow graph Single-cell ATAC-Seq Dimensionality Reduction Analysis

Single-cell ATAC-Seq Dimensionality Reduction Analysis Integrates multiple single-cell ATAC-Seq datasets, reduces dimensionality using LSI.

 https://github.com/datirium/workflows.git

Path: workflows/sc-atac-reduce.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph heatmap-prepare.cwl

Workflow runs homer-maketagdirectory.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/datirium/workflows.git

Path: subworkflows/heatmap-prepare.cwl

Branch/Commit ID: 2d00e7f29c72d33b70dcd46b58db1fc31a7f2d86
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph 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: ddc35c559d1ac6aab4972fe1a2b63300c4373f54
workflow graph samtools_sort

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/samtools_sort.cwl

Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3
workflow graph Single-cell Assign Cell Types

Single-cell Assign Cell Types ============================= Assigns cell types to Seurat clusters.

 https://github.com/datirium/workflows.git

Path: workflows/sc-assign-cell-types.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph picard_markduplicates

Mark duplicates

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 6f16906b30adad5136b0c8135d1e7c07c5741763
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 44ada20f3eeb59005d5bd999d2435102e9bae991