Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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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: e4d6182d5f7a6a880e5f2b21273cf40d25e187df |
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canine_collect_somatic_metrics_module.cwl
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https://github.com/d3b-center/canine-dev.git
Path: subworkflows/canine_collect_somatic_metrics_module.cwl Branch/Commit ID: 7da5645975f5712362cce7908d2ab138e05876fb |
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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: dc6014dc7c1f160ec4ae3d5a57388a6dceaacbc5 |
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germline-gpu-v4.2.0.cwl
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https://github.com/NCGM-genome/WGSpipeline.git
Path: Workflows/germline-gpu-v4.2.0.cwl Branch/Commit ID: b8262067df44ce67268f8af00a043f2187c604bb |
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heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
https://github.com/Barski-lab/workflows.git
Path: subworkflows/heatmap-prepare.cwl Branch/Commit ID: 68ccda2aeaac01375bc25d3994fb1ec44572a63b |
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iwdr-passthrough-successive.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/iwdr-passthrough-successive.cwl Branch/Commit ID: f6aeeae01ca1d821f2be1966f48f5257100f90e5 |
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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: 48381989cb983567ed936fde632714933df65350 |
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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: d09a44ebc8d092ffd8370a324c9e84b37a593d38 |
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protein annotation
Proteins - predict, filter, cluster, identify, annotate |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/protein-filter-annotation.workflow.cwl Branch/Commit ID: 2addcde0f4c1c8547f7f3906c2523cded23e9869 |
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heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
https://github.com/Barski-lab/workflows.git
Path: tools/heatmap-prepare.cwl Branch/Commit ID: 144eee15187c1a1145ce1ee0239da69059fd2752 |
