Explore Workflows
View already parsed workflows here or click here to add your own
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step-valuefrom-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/step-valuefrom-wf.cwl Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf |
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tt_fscr_calls_pass1
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https://github.com/ncbi/pgap.git
Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6 |
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scatter-valuefrom-wf3.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl Branch/Commit ID: 46b7f9766d1bc8a4871474eee25ec730b4e173da Packed ID: main |
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BLASTP, parse, dump FASTA
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https://github.com/ncbi/cwl-demos.git
Path: blast-pipelines/simple_three_step.cwl Branch/Commit ID: master |
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alignment_bwa_mem.cwl
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https://github.com/uc-cdis/genomel_pipelines.git
Path: genomel/cwl/workflows/harmonization/alignment_bwa_mem.cwl Branch/Commit ID: master |
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Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses
Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded. |
https://github.com/datirium/workflows.git
Path: workflows/filter-peaks-for-heatmap.cwl Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081 |
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js-expr-req-wf.cwl#wf
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/js-expr-req-wf.cwl Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a Packed ID: wf |
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scatter-wf4.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/scatter-wf4.cwl Branch/Commit ID: 31aa094dce60cbb176229d6b918bfd5ae09c0390 Packed ID: main |
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align_sort_sa
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https://github.com/ncbi/pgap.git
Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367 |
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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: 34d0ad68878b24aa1ffd8d8b8f7b8b2f5fd82787 |
