Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
QIIME2 Step 1 paired end sequences
QIIME2 Import and Demux Step 1 paired end sequences |
Path: packed/qiime2-step1-import-demux-paired.cwl Branch/Commit ID: qiime2-workflow-paired Packed ID: main |
|
|
|
exome alignment and germline variant detection
|
Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: master |
|
|
|
wf-alignment.cwl
|
Path: somatic/somatic-workflow/wf-alignment.cwl Branch/Commit ID: master |
|
|
|
extract_gencoll_ids
|
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: master |
|
|
|
dynresreq-workflow-inputdefault.cwl
|
Path: v1.0/v1.0/dynresreq-workflow-inputdefault.cwl Branch/Commit ID: master |
|
|
|
upload_results_workflow.cwl
|
Path: workflows/subworkflows/upload_results_workflow.cwl Branch/Commit ID: master |
|
|
|
fastq2fasta-create-bwaindex.cwl
|
Path: cwl/fastq2fasta/fastq2fasta-create-bwaindex.cwl Branch/Commit ID: master |
|
|
|
BD Rhapsody™ Targeted Analysis Pipeline
The BD Rhapsody™ assays are used to create sequencing libraries from single cell transcriptomes. After sequencing, the analysis pipeline takes the FASTQ files and a reference file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file. |
Path: v1.8/rhapsody_targeted_1.8.cwl Branch/Commit ID: master Packed ID: main |
|
|
|
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 |
|
|
|
CGC-subwf.cwl
|
Path: workflows/subworkflows/assembly/CGC-subwf.cwl Branch/Commit ID: master |
