Explore Workflows

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

Graph Name Retrieved From View
workflow graph Alignment without BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 9e5f228bc1a3d0dfe950b5d41d7e4319e834a6d4
workflow graph kfdrc_process_bam.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: subworkflows/kfdrc_process_bam.cwl

Branch/Commit ID: 09c05e788df9cd77cead39892fd02140faa765a8
workflow graph align_sort_sa

https://github.com/ncbi/pgap.git

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
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: 2f0db4b3c515f91c5cfda19c78cf90d339390986
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
workflow graph joint genotyping for trios or small cohorts

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

Path: definitions/subworkflows/joint_genotype.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
workflow graph bact_get_kmer_reference

https://github.com/ncbi/pgap.git

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 4f4448f71645275db5b84eb551990dfe3bf37cbb
workflow graph Transcriptome assembly workflow (paired-end version)

https://github.com/mscheremetjew/workflow-is-cwl.git

Path: workflows/TranscriptomeAssembly-wf.paired-end.cwl

Branch/Commit ID: f059802f5e3601d32ead1fe5b8f24586d8cceaeb