Explore Workflows
View already parsed workflows here or click here to add your own
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Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_ab_initio_training.cwl Branch/Commit ID: dev |
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Detect Docm variants
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https://github.com/genome/cancer-genomics-workflow.git
Path: docm/workflow.cwl Branch/Commit ID: toil_compatibility |
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Water body detection based on NDWI and otsu threshold
Water body detection based on NDWI and otsu threshold |
https://github.com/fabricebrito/fgb.git
Path: wrapped.cwl Branch/Commit ID: main Packed ID: detect_water_body |
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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: master |
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rRNA_selection.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: tools/rRNA_selection.cwl Branch/Commit ID: 3039744 |
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cmsearch-multimodel.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/cmsearch-multimodel.cwl Branch/Commit ID: 0cd2d70 |
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Exome QC workflow
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/qc_exome.cwl Branch/Commit ID: downsample_and_recall |
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scatter_head.cwl
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https://github.com/giannisdoukas/CWLJNIKernel.git
Path: tests/cwl/scatter_head.cwl Branch/Commit ID: master |
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Functional analyis of sequences that match the 16S SSU
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/16S_taxonomic_analysis.cwl Branch/Commit ID: f6b5196 |
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CNV_pipeline
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_workflow/abstract_workflow.cwl Branch/Commit ID: master |
