Explore Workflows

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

Graph Name Retrieved From View
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317
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: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317
workflow graph scatter-wf4.cwl#main

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 596aab620489cd2611f4bc1d9a4fc914ddf34514

Packed ID: main
workflow graph wf-alignment.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: SGDP-recall-CGC/SGDP-recall-cgc/wf-alignment.cwl

Branch/Commit ID: af9a5621efcb44c249697d6df071fe4defe389ac
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
workflow graph Compute library complexity

This workflow compute library complexity

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/bedtools-bam-pbc.cwl

Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317