Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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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: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46 |
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Long-covid.cwl
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https://github.com/cwlviewer-test/Long-covid---aedea650-7a21-11ed-b9d2-e51f21933d80.git
Path: Long-covid.cwl Branch/Commit ID: e6e351cba4bf23073daa00364da5290d3c87738e |
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Dockstore.cwl
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https://github.com/LinkunGao/dock-workflow.git
Path: Dockstore.cwl Branch/Commit ID: 4abae37d554d8a58c146d85544cd3c4d71b200d3 |
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genomics-workspace-transcript.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_genomicsWorkspace/genomics-workspace-transcript.cwl Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f |
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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: 472d453995dcda1b66884c31db562f4fb6094e5a |
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main.cwl
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https://github.com/alpha-unito/cwl-1000genome-workflow.git
Path: main.cwl Branch/Commit ID: 77aaa24c2576826a9a11380b70e84507a53081e8 |
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count-lines7-wf_v1_1.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/count-lines7-wf_v1_1.cwl Branch/Commit ID: 139c64b55f7693d22e6646b8afe585f90da11dcb |
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STAR-Alignment-PE
This workflow aligns the fastq files using STAR for paired-end samples |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/Alignments/star-alignment.cwl Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49 |
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exome alignment with qc, no bqsr, no verify_bam_id
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/exome_alignment_mouse.cwl Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc |
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preprocess_vcf.cwl
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow. |
https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git
Path: preprocess_vcf.cwl Branch/Commit ID: b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb |
