Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass2.cwl Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747 |
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wgs alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_wgs_gvcf.cwl Branch/Commit ID: 25eab0390f6866ce491b44c89d9e0435d228ab6f |
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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: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
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wf_get_peaks_nostats_se.cwl
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https://github.com/YeoLab/eclip.git
Path: cwl/wf_get_peaks_nostats_se.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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strelkaSomaticVariantCaller_v0_1_1.cwl
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https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git
Path: janis_pipelines/wgs_somatic/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl Branch/Commit ID: b4550175be9d485d509c61d87fddf88a8bdb70c1 |
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workflow.cwl
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https://github.com/nal-i5k/organism_onboarding.git
Path: flow_dispatch/2blat/workflow.cwl Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945 |
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Get Proteins
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https://github.com/ncbi/pgap.git
Path: wf_bacterial_prot_src.cwl Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747 |
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taxcheck.cwl
Perform taxonomic identification tasks on an input genome |
https://github.com/ncbi/pgap.git
Path: taxcheck.cwl Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747 |
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AddBamStatsSomatic_v0_1_0.cwl
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https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git
Path: janis_pipelines/wgs_somatic/cwl/tools/AddBamStatsSomatic_v0_1_0.cwl Branch/Commit ID: b4550175be9d485d509c61d87fddf88a8bdb70c1 |
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HS Metrics workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/hs_metrics.cwl Branch/Commit ID: 25eab0390f6866ce491b44c89d9e0435d228ab6f |
