Explore Workflows

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

Graph Name Retrieved From View
workflow graph somatic_exome: exome alignment and somatic variant detection

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 68311dd5328bf6b782a370a0253b41062a3359a3
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 2a81fcde75ca7665814c8de2210c7bc3121a08a3
workflow graph align_and_count_multiple_report.cwl

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/align_and_count_multiple_report.cwl

Branch/Commit ID: 2a1b9d0cbf1fd2b1c9f6faab2ef8254924642b82
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: e509210450e4c62aecb99a228fc97f0eae2d9580
workflow graph genotypegvcfs.cwl

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

Path: genomel/cwl/workflows/variant_calling/genotypegvcfs.cwl

Branch/Commit ID: c661469505c606e1353f23c21a6654724a9d8d63
workflow graph checkm

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

Path: checkm/wf_checkm.cwl

Branch/Commit ID: 2a81fcde75ca7665814c8de2210c7bc3121a08a3
workflow graph Unaligned BAM to BQSR and VCF

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

Path: unaligned_bam_to_bqsr/workflow_no_dup_marking.cwl

Branch/Commit ID: e4c851d65f460e8f48ca184120044fce72cb2433
workflow graph MEME motif

This workflow uses MEME suite for motif finding

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

Path: workflows/ChIP-Seq/meme-motif.cwl

Branch/Commit ID: f9447c1ac522e17531097c93a169a1a31453e874
workflow graph transform_pack.cwl#integrity.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/transform_pack.cwl

Branch/Commit ID: a57b8f0d8708078e87f13297e065d72db10e38a0

Packed ID: integrity.cwl