reference (and plasmid) preprocessing workflow
Version 1

Workflow Type: Common Workflow Language

**Workflow for preprocessing a reference file. **

Steps:
-When a GenBank file is not provided, it is downloaded from NCBI based on a accession number.
-When multiple plasmid GenBank files are provided, they are merged into one file.
-When any amount of plasmid GenBank files are provided, the reference is merged with the plasmid GenBank file(s) into one file. A FASTA file is also extracted.
-When no plasmid Genbank files are provided, a FASTA file is extracted from the reference GenBank file.
-A GFF3 file is extracted from the final GenBank file.
-The final step determines the relevant outputs.

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

Click and drag the diagram to pan, double click or use the controls to zoom.

SEEK ID: https://workflowhub.eu/workflows/1818?version=1

Inputs

ID	Name	Description	Type
accession_number	accession number	accession number, used to download a GenBank file from NCBI, mandatory when not inputting a reference file.	string
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.	File
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.	File
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.	File
plasmids	plasmid file(s)	Input plasmid GenBank files.	array containing File
reference_file	reference GenBank file	Reference file in GenBank format.	File

Steps

ID	Name	Description
determine_output	determine output	Determines relevant final outputs.
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.
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.

Outputs

ID	Name	Description	Type
fasta_final	FASTA output file	Final FASTA output file.	File
genbank_final	GenBank output file	Final GenBank output file.	File
gff3	GFF3 output file	Final GFF3 output file.	File