Explore Workflows
View already parsed workflows here or click here to add your own
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checker_workflow_wrapping_workflow.cwl
This demonstrates how to wrap a \"real\" workflow with a checker workflow that runs both the tool and a tool that performs verification of results |
https://github.com/dockstore-testing/dockstore-workflow-md5sum-unified.git
Path: checker_workflow_wrapping_workflow.cwl Branch/Commit ID: develop |
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Illumina read quality control, trimming and contamination filter.
**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple paired datasets will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - BBduk for phiX and (optional) rRNA filtering<br /> - Kraken2 for taxonomic classification of reads (optional)<br /> - BBmap for (contamination) filtering using given references (optional)<br /> - FastQC on filtered (merged) data<br /> **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_illumina_quality.cwl Branch/Commit ID: master |
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basename-fields-test.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/basename-fields-test.cwl Branch/Commit ID: master |
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CroMaSt.cwl
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https://gitlab.inria.fr/capsid.public_codes/CroMaSt.git
Path: CroMaSt.cwl Branch/Commit ID: main |
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count-lines15-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines15-wf.cwl Branch/Commit ID: master |
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ChIP-exo peak caller workflow for single-end samples with no P-Value inflection
This workflow execute peak caller and QC from ChIP-exo for single-end samples with no P-Value inflection |
https://gitlab.com/r78v10a07/cwl-workflow.git
Path: workflows/ChIP-exo/peak_caller-SE-no_inflection.cwl Branch/Commit ID: master |
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rRNA_selection.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: tools/rRNA_selection.cwl Branch/Commit ID: 3039744 |
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Nanopore Quality Control and Filtering
**Workflow for nanopore read quality control and contamination filtering.** - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 read filtering based on given references - FastQC after filtering (read quality control) **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_nanopore_quality.cwl Branch/Commit ID: master |
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wf.cwl#VDJ_Assemble_and_Annotate_Contigs_IG.cwl
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https://github.com/aheinzel/tmp_rhapsody_for_cwl_vis.git
Path: wf.cwl Branch/Commit ID: main Packed ID: VDJ_Assemble_and_Annotate_Contigs_IG.cwl |
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SSU-from-tablehits.cwl
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https://github.com/proteinswebteam/ebi-metagenomics-cwl.git
Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 3168316 |
