Explore Workflows

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

Graph Name Retrieved From View
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph blastp_wnode_struct

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

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: 61eaea2f746c8a1fc2a2b731056b068e28ca4e20
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph gk-parse-current.cwl

https://github.com/vdikan/cwl-gk-thermal.git

Path: cwl/gk-parse-current.cwl

Branch/Commit ID: 48f4b8266a5a199cfc100d45148996f10a092f3b
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: ef7f3345b352319ec22dffba26c79df033b141f9
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: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: add6b7724698694e0e72d972e2e85e1ae4e67902