reference (and plasmid) preprocessing workflow
Version 1

Workflow Type: Common Workflow Language

Workflow 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.

This workflow on WorkflowHub: https://workflowhub.eu/projects/upcoming

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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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