Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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Build Bowtie indices
Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome |
https://github.com/datirium/workflows.git
Path: workflows/bowtie-index.cwl Branch/Commit ID: 2f0db4b3c515f91c5cfda19c78cf90d339390986 |
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kmer_seq_entry_extract_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: 75ea689c0a8c9902b4598b453455857cb08e885a |
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Build Bismark indices
Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input. |
https://github.com/datirium/workflows.git
Path: workflows/bismark-index.cwl Branch/Commit ID: a839eb6390974089e1a558c49fc07b4c66c50767 |
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gathered exome alignment and somatic variant detection for cle purpose
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_exome_cle_gathered.cwl Branch/Commit ID: 87faba2fff8007ecc95160729b1c7cd0376e46f2 |
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Bisulfite QC tools
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bisulfite_qc.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f |
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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: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a |
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strelka workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/strelka_and_post_processing.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f |
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process VCF workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/strelka_process_vcf.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a |
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exome alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_exome.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a |
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aggregate_visualize
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https://github.com/msk-access/qc_generation.git
Path: access_qc__packed.cwl Branch/Commit ID: 248e7c3edaff48e1b97a7931d66aa3b23ce97f54 Packed ID: aggregate_visualize.cwl |