plasmid preprocessing workflow
Download RO-CrateWorkflow for preprocessing the reference file. Downloads the GenBank file from NCBI if not provided, concatenates plasmid GenBank file(s) with each other and the reference file, extracts GFF3 from the (merged) reference.
This workflow on WorkflowHub: https://workflowhub.eu/workflows/1818
All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/tools Workflows: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/workflows
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| reference_file | reference GenBank file | Reference file in GenBank format. |
|
| accession_number | accession number | accession number, used to download a GenBank file from NCBI, mandatory when not inputting a reference file. |
|
| plasmids | plasmid file(s) | Input plasmid GenBank files. |
|
| merging_genbank_script | merging script | Python script to merge multiple GenBank Files. Passed externally within the git structure to avoid having to host a new image. |
|
| fasta_extraction_script | FASTA extraction script | Python script that extracts a FASTA file from GenBank Files. Passed externally within the git structure to avoid having to host a new image. |
|
| gff3_extraction_script | GFF3 extraction script | BioPerl script that extracts a GFF3 file from GenBank Files. Passed externally within the git structure to avoid having to host a new image. |
|
Steps
| ID | Name | Description |
|---|---|---|
| fetch_reference | fetch reference | Downloads the associated GenBank file from the supplied accession number. |
| merge_plasmids | merge plasmids | Merges plasmids when more than one are present. |
| merge_reference | merge plasmid(s) with reference | Merges the plasmid(s) with the reference GenBank file. |
| extract_fasta | extract FASTA | Extracts FASTA file from input reference file when no plasmids are provided. |
| extract_gff3 | extract GFF3 | Extracts GFF3 annotation file from the (merged) reference. |
| determine_output | determine output | Determines relevant final outputs. |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| genbank_final | GenBank output file | Final GenBank output file. |
|
| fasta_final | FASTA output file | Final FASTA output file. |
|
| gff3 | GFF3 output file | Final GFF3 output file. |
|
Version History
Version 2 (latest) Created 9th Jul 2026 at 13:39 by Martijn Melissen
force UTF-8 encoding, add FASTA output
Frozen
Version-209715e6
Version 1 (earliest) Created 22nd Jul 2025 at 16:22 by Martijn Melissen
Frozen
Version-1
1c0d264
Creators and Submitter
Views: 1574 Downloads: 390
Created: 22nd Jul 2025 at 16:22
Last updated: 14th Jul 2026 at 09:48
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The Laboratory of Systems and Synthetic Biology (SSB) contributes to elucidate mechanisms underlying basic cellular processes, evolution and interactions among microbes and between microbes and their environment (including the human host). We do so in the context of entire biological systems. We translate the acquired knowledge into biotechnological, medical and environmental applications.
