Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
ani_top_n
|
Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: 03cfa6b27e502bda00ceb57b8bd5017076effd45 |
|
|
|
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 |
Path: cwl/workflows/workflow_nanopore_quality.cwl Branch/Commit ID: master |
|
|
|
tt_fscr_calls_pass1
|
Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3 |
|
|
|
Genome conversion and annotation
Workflow for genome annotation from EMBL format |
Path: cwl/workflows/workflow_sapp_microbes.cwl Branch/Commit ID: master |
|
|
|
Quality assessment, amplicon classification
Workflow for quality assessment of paired reads and classification using NGTax 2.0. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Export module |
Path: cwl/workflows/workflow_ngtax.cwl Branch/Commit ID: master |
|
|
|
Metagenomics workflow
Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon |
Path: cwl/workflows/workflow_pilon_mapping.cwl Branch/Commit ID: master |
|
|
|
Quality assessment, amplicon classification and functional prediction
Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax |
Path: cwl/workflows/workflow_ngtax_picrust2.cwl Branch/Commit ID: master |
|
|
|
kmer_seq_entry_extract_wnode
|
Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3 |
|
|
|
SAMSA2 pipeline
SAMSA2 complete workflow for meta-omics read annotation Steps: - Diamond read blastx - Refseq - SEED - SAMSA2 processing |
Path: cwl/workflows/workflow_samsa2.cwl Branch/Commit ID: master |
|
|
|
basename-fields-test.cwl
|
Path: tests/basename-fields-test.cwl Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4 |
