Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph alignment_bwa_mem_no_trim.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_bwa_mem_no_trim.cwl

Branch/Commit ID: f55f0011de7db66f873ffb0f700f3fe26b33911e

workflow graph Apply filters to VCF file

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: 3a287b7cb6162cdea79865235d224fea45963d87

workflow graph Apply filters to VCF file

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec

workflow graph Apply filters to VCF file

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: 509938802c5e42bb8084c6a5a26ab6425c60e69a

workflow graph umi molecular alignment workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec

workflow graph umi molecular alignment workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405

workflow graph umi molecular alignment workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6

workflow graph bam to trimmed fastqs and HISAT alignments

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec

workflow graph 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: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df

workflow graph Run pindel on provided region

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6