Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
js-expr-req-wf.cwl#wf
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534 Packed ID: wf |
|
|
|
group-isoforms-batch.cwl
Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored. |
https://github.com/datirium/workflows.git
Path: tools/group-isoforms-batch.cwl Branch/Commit ID: 77970404d7c704cba965ae646582e19e5d76aabe |
|
|
|
waltz-workflow.cwl
|
https://github.com/mskcc/Innovation-Pipeline.git
Path: workflows/waltz/waltz-workflow.cwl Branch/Commit ID: 4797e94233677c0dfe1e8226d15d9b1ff7634161 |
|
|
|
Prepare user input
Prepare user input for NCBI-PGAP pipeline |
https://github.com/ncbi/pgap.git
Path: prepare_user_input2.cwl Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8 |
|
|
|
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: 822a07cd6937faa4be377b0cac8780f52c817faf |
|
|
|
conflict-wf.cwl#collision
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl Branch/Commit ID: f997d13af87216e9b5048c732a511053c7ba714c Packed ID: collision |
|
|
|
standard_pipeline.cwl
This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2 |
https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/standard_pipeline.cwl Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0 |
|
|
|
ROSE: rank ordering of super-enhancers
Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff) |
https://github.com/datirium/workflows.git
Path: workflows/super-enhancer.cwl Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9 |
|
|
|
module-3.cwl
|
https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/module-3.cwl Branch/Commit ID: 5bf88423593441e4bf6b432111160446cd8dcf13 |
|
|
|
qc_workflow_wo_waltz.cwl
This workflow is intended to be used to test the QC module, without having to run the long waltz step |
https://github.com/andurill/ACCESS-Pipeline.git
Path: workflows/QC/qc_workflow_wo_waltz.cwl Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f |
