Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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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: 767e3dc7448da5bc44e4817c4161f6e4530032e2 |
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raw-reads-1.cwl
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https://github.com/EBI-Metagenomics/pipeline-v5.git
Path: workflows/conditionals/raw-reads/raw-reads-1.cwl Branch/Commit ID: fff6fa392370b56e1fe7c374167ba73df3018775 |
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tt_fscr_calls_pass1
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https://github.com/ncbi/pgap.git
Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: 89839cdb0a3216024f5f97af5581ae9753de0496 |
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format_rrnas_from_seq_entry
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https://github.com/ncbi/pgap.git
Path: task_types/tt_format_rrnas_from_seq_entry.cwl Branch/Commit ID: 5c40c5a0464c84076e0e407a0e05522b43bdc0a6 |
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Nanopore assembly workflow
**Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning**<br> - Workflow Nanopore Quality - Kraken2 taxonomic classification of FASTQ reads - Flye (de-novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) **When Illumina reads are provided:** - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - Assembly polishing with Pilon<br> - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2 - CheckM - BUSCO - GTDB-Tk **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> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br> |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_nanopore_assembly.cwl Branch/Commit ID: master |
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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: f390475a4e0898d4933f0a28dae278aa35803eb1 |
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taxonomy_check_16S
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https://github.com/ncbi/pgap.git
Path: task_types/tt_taxonomy_check_16S.cwl Branch/Commit ID: f390475a4e0898d4933f0a28dae278aa35803eb1 |
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tt_kmer_top_n.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: f390475a4e0898d4933f0a28dae278aa35803eb1 |
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Align reference proteins plane complete workflow, with miniprot
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_protein_alignment_miniprot.cwl Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3 |
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Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/pvacseq.cwl Branch/Commit ID: e509210450e4c62aecb99a228fc97f0eae2d9580 |
