CWL Workflow: Subworkflow for Annotation

Workflow: Subworkflow for Annotation

Fetched 2025-10-23 00:25:31 GMT

Verified with cwltool version 3.1.20230201224320

\"Subworkflow for Metagenome Annotation This subworkflow is for annotation of predicted protein coding sequences. \"

This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

ID	Type	Title	Doc
SW_EVALUE	Float	evalue	E-value threshold of BLASTP (diamond) and BLASTN alignment
SW_THREADS	Integer	threads	number of threads to use in this subworkflow
SW_DIAMOND_INDEX_FILE	File	Protein fasta file for diamond index	Protein fasta file for diamond index
SW_OUTPUT_GTF_FILE_NAME	String	Output GTF file name	Output GTF file name
SW_BLASTN_rRNA_FASTA_FILE1	File	SILVA_138.1_LSUParc_tax_silva	SILVA_138.1_LSUParc_tax_silva
SW_BLASTN_rRNA_FASTA_FILE2	File	SILVA_138.1_SSUParc_tax_silva	SILVA_138.1_SSUParc_tax_silva
SW_PRODIGAL_RESULT_DNA_FASTA_FILE	File	input fasta file (nucleotide sequence generated by prodigal process)	predicted protein coding sequences produced by Prodigal process
SW_PRODIGAL_RESULT_PROTEIN_FASTA_FILE	File	predicted protein coding sequences produced by Prodigal process	predicted protein coding sequences produced by Prodigal process

ID	Runs	Label	Doc
PROCESS_BLASTN_rRNA	blastn_rRNA_ssw.cwl (Workflow)	rRNA annotation workflow with scatter processing	\"This workflow performs rRNA annotation processing for multiple index files using scatter. It executes 4 processes: makeblastdb, blastn alignment, filtering, and rRNA removal for each rRNA index file. related CWL file: ./Tools/09_makeblastdb_rRNA.cwl ./Tools/10_blastn_rRNA_alignment.cwl ./Tools/10_blastn_rRNA_filter1.cwl ./Tools/10_blastn_rRNA_filter2.cwl ./Tools/10_blastn_rRNA_filter3.cwl\"
PROCESS_GTF_CREATION	../Tools/12_faablast2gtf4tpm.cwl (CommandLineTool)	gtf file creation	\"annotaion informtaion file (gtf formtaed) creation from the results of BLASTN and DIAMOND original script: scripts/07_annotation_modified.sh original command: 07_1_faablast2gtf4tpm.py --faa ${f}.faa --rrna ${f}_rRNAlist.txt --uniprot ${f}-rRNA_uniprot.txt -o ${f}_annotation.gtf\"
PROCESS_DIAMOND_PROTEIN	diamond_protein_ssw.cwl (Workflow)	diamond proteinworkflow	\"This workflow performs diamond protein alignment process for predicted protein sequences. It executes 2 processes: diamond index creation and diamond alignment. related CWL file: ./Tools/09_diamond_index.cwl ./Tools/11_diamond_uniprot_alignment.cwl ./Tools/11_diamond_uniprot_filter1.cwl ./Tools/11_diamond_uniprot_filter2.cwl\"

ID	Type	Label	Doc
OUTPUT_GTF_FILE	File	Output GTF file	Output GTF file

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