Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 8a8fffb78b1e327ba0da51840ac8acc0c218d611
workflow graph Creates FASTA file from BED coordinates

This workflow creates FASTA file from BED coordinates

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/fasta-from-bed.cwl

Branch/Commit ID: e1c19e64f6fc210f65472ee227786d33c9b4909a
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 9abcceb95c8dcb74b98d7eeda265d8f3a9a4329e