Explore Workflows
View already parsed workflows here or click here to add your own
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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: 1e7aa9f0c34987ddafa35f9b1d2c77d99fafbdab |
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Production Configuration
This workflow prepares the configuration of the subsequent production steps. |
https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git
Path: workflows/wms/uc-wms-XXX.cwl Branch/Commit ID: eb6a98289850791cd1891c89e5209180c35c7858 |
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chipseq-gen-bigwig.cwl
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https://github.com/datirium/workflows.git
Path: subworkflows/chipseq-gen-bigwig.cwl Branch/Commit ID: 0ddfca10c41f83bb120c7633e0db9dba7441bca0 |
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directory.cwl
Inspect provided directory and return filenames. Generate a new directory and return it (including content). |
https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/directory.cwl Branch/Commit ID: 8ef515037de411abd2f84b569ad4d4a4f7a2c7a0 |
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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: c5bae2ca862c764911b83d1f15ff6af4e2a0db28 |
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Exome QC workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315 |
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tt_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 72c3091012f5c2dce38ad9213cda617d2c7a61ac |
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kmer_cache_store
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: d87a0786b52809b36201adb7d3d3ab2b8bbbef20 |
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allele-process-strain.cwl
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https://github.com/Barski-lab/workflows.git
Path: subworkflows/allele-process-strain.cwl Branch/Commit ID: f2aee86fecd321efc6857b124350f079238ea2ba |
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wgs alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/wgs_alignment.cwl Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c |
