Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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Produce a list of residue-mapped structural domain instances from CATH ids
Retrieve and process the PDB structures corresponding to the CATH superfamily ids resulting in a list of residue-mapped structural domain instances along with lost structural instances (requires Data/cath_domain_description_file.txt downloaded from CATH and uses SIFTS resource for PDB to UniProt residue Mapping) |
https://github.com/HrishiDhondge/CroMaSt.git
Path: Tools/resmapping_cath_instances_subwf.cwl Branch/Commit ID: main |
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RNA-Seq alignment and transcript/gene abundance workflow
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https://github.com/genome/cancer-genomics-workflow.git
Path: rnaseq/workflow.cwl Branch/Commit ID: toil_compatibility |
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word-mapping-dir.cwl#align-texts-wf.cwl
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https://github.com/KBNLresearch/ochre.git
Path: ochre/cwl/word-mapping-dir.cwl Branch/Commit ID: master Packed ID: align-texts-wf.cwl |
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Hmmscan
Run hmmscan over an array of files (supports empty or non existent files). Each file will be chunked in 1000 sequences per file to improve the performance. The output will be the concatenation of the output tables. |
https://github.com/EBI-Metagenomics/emg-viral-pipeline.git
Path: cwl/src/Tools/HMMScan/hmmscan_swf.cwl Branch/Commit ID: master |
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rnaediting2strands.workflow.cwl
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https://github.com/YeoLab/sailor.git
Path: CWL-SINGULARITY-pipeline-building-code/cwl/rnaediting2strands.workflow.cwl Branch/Commit ID: 6f21086 |
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Detect Variants workflow for nonhuman WGS pipeline
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/detect_variants_wgs_nonhuman.cwl Branch/Commit ID: master |
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exome alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: master |
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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/litd/analysis-workflows.git
Path: definitions/pipelines/somatic_exome.cwl Branch/Commit ID: master |
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hisat2_index.cwl
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https://github.com/rawgene/cwl.git
Path: workflows/hisat2_index.cwl Branch/Commit ID: master |
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wf_contam_detect.cwl
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https://github.com/ncbi/pipelines.git
Path: contam_filter/wf_contam_detect.cwl Branch/Commit ID: master |