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: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: 5282690e0f634a5f83107ba878fe62cbbb347408
workflow graph rRNA_selection.cwl

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 8fb4ac7f5a66897206c7469101a471108b06eada
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 861d9baa067af98d794ba0ed4e43aa42e37d8a24
workflow graph bismark-methylation-se.cwl

Bismark Methylation pipeline. We can use indices_folder as genome_folder for bismark_extract_methylation step, because it insludes the original FASTA files too.

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

Path: workflows/bismark-methylation-se.cwl

Branch/Commit ID: cf84038de256c7ca98657ad81734d1aca1dad8c1
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 861d9baa067af98d794ba0ed4e43aa42e37d8a24