Explore Workflows

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

Graph Name Retrieved From View
workflow graph SetArrayElementCoordinates

Transform array element coordinates into the coordinate system required by the simulation pipeline (i.e., CORSIKA system).

 https://gitlab.desy.de/gernot.maier/cwlsandbox.git

Path: workflows/SetArrayElementCoordinates.cwl

Branch/Commit ID: 87d54f769e6dd3b56b99ca4038d8e0335b4acedc
workflow graph module-1.cwl

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/module-1.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph bam_filtering

BAM filtering

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

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3
workflow graph alignment_prep.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_prep.cwl

Branch/Commit ID: 7504ead048c3acd64b9b92e44d044d558cb696f2
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 8a8fffb78b1e327ba0da51840ac8acc0c218d611
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph timelimit2-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/timelimit2-wf.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
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: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a