Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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Align reference proteins plane complete workflow, with miniprot
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_protein_alignment_miniprot.cwl Branch/Commit ID: 8af4e2aabf43d5e3c7162efae4ad4649df5601e2 |
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mut2.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/mut2.cwl Branch/Commit ID: 1338ffbf2492a2ca1be1d7c5c46597bd9205aa24 |
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tt_kmer_top_n.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: 5d5c4b4ed6d6de42eda2c68aefcf738c201517fb |
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ani_top_n
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https://github.com/ncbi/pgap.git
Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: 5d5c4b4ed6d6de42eda2c68aefcf738c201517fb |
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kmer_build_tree
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_build_tree.cwl Branch/Commit ID: 5d5c4b4ed6d6de42eda2c68aefcf738c201517fb |
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kmer_top_n_extract
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n_extract.cwl Branch/Commit ID: 5d5c4b4ed6d6de42eda2c68aefcf738c201517fb |
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gcaccess_from_list
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https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 5d5c4b4ed6d6de42eda2c68aefcf738c201517fb |
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kmer_ref_compare_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: 5d5c4b4ed6d6de42eda2c68aefcf738c201517fb |
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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/Barski-lab/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 1d45ce42181dfce7aceec8bc99a3730eb5285948 |
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Create Genomic Collection for Bacterial Pipeline, ASN.1 input
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https://github.com/ncbi/pgap.git
Path: genomic_source/wf_genomic_source_asn.cwl Branch/Commit ID: 6a456869b53513bff31fec02cc5ea3cc26fede36 |
