Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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Merge, annotate, and generate a TSV for SVs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31 |
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Execute CRISPR
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https://github.com/ncbi/pgap.git
Path: bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23 |
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qiime2 identify differentially abundant features
Differential abundance testing with ANCOM from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
https://github.com/Duke-GCB/bespin-cwl.git
Path: packed/qiime2-step2-deblur.cwl Branch/Commit ID: 777dbcd05b5d115371dcda6d54ebaf75dae8afb8 Packed ID: qiime2-09-ancom.cwl |
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foldseek easy-search workflow
foldseek easy-search workflow listing files and foldseek easy-search process |
https://github.com/yonesora56/plant2human.git
Path: Workflow/10_foldseek_easy_search_wf.cwl Branch/Commit ID: 4fc824b36b986af931cc136be7a91355b772b39b |
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scatter GATK HaplotypeCaller over intervals
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https://github.com/apaul7/cancer-genomics-workflow.git
Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d |
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group-isoforms-batch.cwl
Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored. |
https://github.com/datirium/workflows.git
Path: tools/group-isoforms-batch.cwl Branch/Commit ID: 29bf638904709cfbf10908adcd51ba4886ace94a |
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count-lines7-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl Branch/Commit ID: 6e9f82a6d2195d4f16f28fd6e1485138372fb430 |
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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: 94f3486d3867b9ece47c07bc8fe47f57569786f4 |
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spurious_annot pass2
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https://github.com/ncbi/pgap.git
Path: spurious_annot/wf_spurious_annot_pass2.cwl Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23 |
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spurious_annot
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https://github.com/ncbi/pgap.git
Path: spurious_annot/wf_spurious_annot_pass1.cwl Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23 |
