Explore Workflows

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

Graph Name Retrieved From View
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/exome_alignment_mouse.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants_mouse.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph example_workflow.cwl

Example CWL workflow that uses some advanced features

https://github.com/mskcc/pluto-cwl.git

Path: cwl/example_workflow.cwl

Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph basename-fields-test.cwl

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

Path: cwltool/schemas/v1.0/v1.0/basename-fields-test.cwl

Branch/Commit ID: ecdfe1ee769d05790f70ac87a711131f441f3753
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_mouse.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph protein annotation

Proteins - predict, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-annotation.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a
workflow graph allele-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: 01c6af7a598eb44f6bcaa9b5eecf13229f28546e
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49