Explore Workflows
View already parsed workflows here or click here to add your own
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databkgmc.cwl
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Path: cwl/databkgmc.cwl Branch/Commit ID: pack_test |
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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> |
Path: cwl/workflows/workflow_nanopore_assembly.cwl Branch/Commit ID: master |
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sequence (bam or fastqs) to trimmed fastqs
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Path: definitions/subworkflows/sequence_to_trimmed_fastq.cwl Branch/Commit ID: low-vaf |
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tt_univec_wnode.cwl
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Path: task_types/tt_univec_wnode.cwl Branch/Commit ID: dev |
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post-proccessing-go-pfam-stats-subwf.cwl
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Path: workflows/subworkflows/functional-annotation/post-proccessing-go-pfam-stats-subwf.cwl Branch/Commit ID: eosc-life-gos |
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Chunked version of phmmer-v3.2.cwl
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Path: workflows/phmmer-v3.2-chunked-wf.cwl Branch/Commit ID: master |
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qiime2 explore sample taxonomic composition
Taxonomic analysis from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
Path: packed/qiime2-step2-dada2-paired.cwl Branch/Commit ID: qiime2-workflow-paired Packed ID: qiime2-08-taxonomic-analysis.cwl |
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Functional analyis of sequences that match the 16S SSU
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Path: workflows/16S_taxonomic_analysis.cwl Branch/Commit ID: f993cad |
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Transcripts annotation workflow
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Path: workflows/TranscriptsAnnotation-i5only-wf.cwl Branch/Commit ID: cwlexec |
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qa_check_subwf.cwl
This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs |
Path: qa_check_subwf.cwl Branch/Commit ID: master |
