Explore Workflows

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6

Set light guide efficiency as function of wavelength and incident angle.

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

Path: workflows/SetLightGuideEfficiency.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

https://github.com/kids-first/kf-dev-single-cell-rna.git

Path: workflows/kf_STAR_Solo_10x_alignment_wf.cwl

Branch/Commit ID: 8c1d2315ad46fe0a30bf618e108e55b0263c7c6d

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

Path: testdata/workflow_input_sf_expr_array.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7

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: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

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

Path: testdata/workflow_input_sf_expr_array_v1_1.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_sentieon_alignment_wf.cwl

Branch/Commit ID: 0e35fb09e15a7a6af52d9906111136a961b2c488

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375

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

Path: definitions/pipelines/immuno.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622