Explore Workflows

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

Graph Name Retrieved From View
workflow graph PGAP Pipeline, simple user input, PGAPX-134

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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

Path: pgap.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
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: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
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: 42c66dd24ce5026d3f717214ddb18b7b4fae93cf
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph tt_kmer_compare_wnode

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58