Explore Workflows

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

Graph Name Retrieved From View
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph 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: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

 https://github.com/datirium/workflows.git

Path: workflows/bowtie-index.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph ROSE: rank ordering of super-enhancers

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

 https://github.com/datirium/workflows.git

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
workflow graph Creates FASTA file from BED coordinates

This workflow creates FASTA file from BED coordinates

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

Path: workflows/File-formats/fasta-from-bed.cwl

Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph Per-chromosome pindel

https://github.com/genome/cancer-genomics-workflow.git

Path: pindel/pindel_cat.cwl

Branch/Commit ID: e4c851d65f460e8f48ca184120044fce72cb2433
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305