Explore Workflows

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

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

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

Path: definitions/pipelines/gathered_somatic_exome.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph allele-vcf-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/Barski-lab/workflows.git

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

Branch/Commit ID: 68ccda2aeaac01375bc25d3994fb1ec44572a63b
workflow graph record-output-wf_v1_1.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/record-output-wf_v1_1.cwl

Branch/Commit ID: c46a3ad4e488e75b7a58032c129f0605f5e84f40
workflow graph kfdrc_alignment_fqinput_CramOnly_wf.cwl

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

Path: workflows/kfdrc_alignment_fqinput_CramOnly_wf.cwl

Branch/Commit ID: b6d3cf83b57011983fb848c7178017e07b94c270
workflow graph Bisulfite alignment and QC

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: 72e0bdc1ec449d86df4534132e9a30ad7e9b8afd
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: ac387721a55fd91df3dcdf16e199354618b136d1
workflow graph sum-wf-noET.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/sum-wf-noET.cwl

Branch/Commit ID: 5e3fac092a720c5670ae3e787eabe1aaade71d83
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: db0a91eb094d0a7c58042d4264986ea042dd4827
workflow graph chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: 5a92b026bd62fe1597de940088e8adeef6939d5a
workflow graph workflow_input_sf_expr_v1_1.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/workflow_input_sf_expr_v1_1.cwl

Branch/Commit ID: 141048ae4b78aa765782bb752be4a1550edc2eea