Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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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: 9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e |
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wf_clipseqcore_pe_2barcodes.cwl
Workflow for handling reads containing two barcodes. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_clipseqcore_pe_2barcodes.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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kallisto_wf_se.cwl
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https://github.com/pitagora-network/pitagora-cwl.git
Path: workflows/kallisto/single_end/kallisto_wf_se.cwl Branch/Commit ID: 14c76e15665ef0566eae5c2be75dba7feb74a50b |
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workflow.cwl
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https://github.com/Andreja28/cloud-workflows.git
Path: cwl/pak-fs/workflow.cwl Branch/Commit ID: b2d5b67c9bbc0cce97dcf65f3cdc8da2c156e145 |
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cnv_manta
CNV Manta calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/cnv_manta.cwl Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa |
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cnv_gridss
CNV GRIDSS calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/cnv_gridss.cwl Branch/Commit ID: d07f44fc5c253dc4044d86ea79ac6f9e03c01bfa |
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genomics-workspace-protein.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_genomicsWorkspace/genomics-workspace-protein.cwl Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945 |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31 |
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cnv_exomedepth
CNV ExomeDepth calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3 |
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workflow-fasta-pratt.cwl
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https://github.com/ebi-wp/webservice-cwl.git
Path: workflows/workflow-fasta-pratt.cwl Branch/Commit ID: 5df6b762980b15b0f6389149311b82bdd6dff37d |