Explore Workflows
View already parsed workflows here or click here to add your own
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umi molecular alignment workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe |
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Cell Ranger Aggregate (ATAC)
Cell Ranger Aggregate (ATAC) Combines outputs from multiple runs of “Cell Ranger Count (ATAC)” pipeline. |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-atac-aggr.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895 |
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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: 30031ca5e69cec603c4733681de54dc7bffa20a3 |
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scatter-valuefrom-wf3.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c Packed ID: main |
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exome alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/exome_alignment.cwl Branch/Commit ID: f21b6c6f70f01d0fe08193684060161107f0bf59 |
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bams2gvcf.wBQSR.cwl
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https://github.com/ddbj/human-reseq.git
Path: Workflows/bams2gvcf.wBQSR.cwl Branch/Commit ID: 9064c301d858a796f8340d1e762e5916fd199da0 |
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abra_workflow.cwl
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https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/ABRA/abra_workflow.cwl Branch/Commit ID: 5bf88423593441e4bf6b432111160446cd8dcf13 |
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bqsr_workflow.cwl
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https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/BQSR/bqsr_workflow.cwl Branch/Commit ID: 5bf88423593441e4bf6b432111160446cd8dcf13 |
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extract_readgroup_fastq_se.cwl
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https://github.com/nci-gdc/gdc-dnaseq-cwl.git
Path: workflows/bamfastq_align/extract_readgroup_fastq_se.cwl Branch/Commit ID: 6b43e8b03256492f2b36ffcf548704daaafee6f6 |
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xenbase-sra-to-fastq-se.cwl
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https://github.com/Barski-lab/workflows.git
Path: subworkflows/xenbase-sra-to-fastq-se.cwl Branch/Commit ID: afbec98437a7796a509fffbad8c3370aa099f059 |
