CWL Workflow: rRNA annotation workflow with scatter processing

Workflow: rRNA annotation workflow with scatter processing

Fetched 2025-10-23 12:39:24 GMT

Verified with cwltool version 3.1.20230201224320

\"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\"

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Inputs/Outputs

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.

Inputs

ID	Type	Title	Doc
EVALUE	Float	evalue	E-value threshod of BLASTN search
THREADS	Integer	threads	number of threads to use
MAX_TARGET_SEQS	Integer	max target seqs	number of annotaion output for each DNA sequences, sometimes annotaiton output will be more than 1 even though the setting is 1
INPUT_FASTA_FILE	File	input fasta file (nucleotide sequence generated by prodigal process)	predicted protein coding sequences produced by Prodigal process
OUTPUT_FILE_NAME1	String	output file name	text file of annotaion information of contaminating rRNA
OUTPUT_FILE_NAME2	String	output file name	text file of annotaion information of contaminating rRNA
BLASTN_rRNA_FASTA_FILE1	File	SILVA_138.1_LSUParc_tax_silva	\"rRNA file for SILVA_138.1_LSUParc_tax_silva You must obtain the file in advance from the following link. https://ftp.arb-silva.de/release_138.1/Exports/SILVA_138.1_LSUParc_tax_silva.fasta.gz\"
BLASTN_rRNA_FASTA_FILE2	File	SILVA_138.1_SSUParc_tax_silva	\"rRNA file for SILVA_138.1_SSUParc_tax_silva You must obtain the file in advance from the following link. https://ftp.arb-silva.de/release_138.1/Exports/SILVA_138.1_SSUParc_tax_silva.fasta.gz\"
BLASTN_rRNA_INDEX_DIR_NAME1	String	SILVA_138.1_LSUParc_tax_silva (directory name)	\"rRNA index directory name for SILVA_138.1_LSUParc_tax_silva\"
BLASTN_rRNA_INDEX_DIR_NAME2	String	SILVA_138.1_SSUParc_tax_silva (directory name)	\"rRNA index directory name for SILVA_138.1_SSUParc_tax_silva\"
PRODIGAL_RESULT_PROTEIN_FASTA_FILE	File	prodigal result protein fasta file	predicted protein sequences of Prodigal output

Steps

ID	Runs	Label	Doc
BLASTN_rRNA_FILTER1	../Tools/10_blastn_rRNA_filter1.cwl (CommandLineTool)	blastn result file filter	\"This tool is used to filter blastn result. BLASTN result text file contains annotation of rRNA. Sometimes, more than one rRNA are annotated to one query sequence, it should be fixed for gft file production. Also, later process needs rRNA annotated predicted coding sequences list. original script: scripts/07_annotation_modified.sh original command1: cat ${f}_*.txt \| awk '!x[$1]++' > ${f}_rRNAlist.txt original command2: cut -f1 ${f}_rRNAlist.txt \| sort > ${f}_rRNA_toplist.txt\"
BLASTN_rRNA_FILTER2	../Tools/10_blastn_rRNA_filter2.cwl (CommandLineTool)	blastn result file filter	\"This tool is used to filter blastn result. original script: scripts/07_annotation_modified.sh original command: seqkit grep -v -f ${f}_rRNA_toplist.txt ${f}.faa > ${f}-rRNA.faa\"
MAKEBLASTDB_SILVA_138.1_LSUParc_tax_silva	../Tools/09_makeblastdb_rRNA.cwl (CommandLineTool)	makeblastdb command for rRNA database creation	\"This tool is used to create a blast database from a fasta file.\"
MAKEBLASTDB_SILVA_138.1_SSUParc_tax_silva	../Tools/09_makeblastdb_rRNA.cwl (CommandLineTool)	makeblastdb command for rRNA database creation	\"This tool is used to create a blast database from a fasta file.\"
BLASTN_rRNA_alignment_silva_138.1_LSUParc_tax_silva	../Tools/10_blastn_rRNA_alignment.cwl (CommandLineTool)	blastn command for rRNA database creation	\"This tool is used to execute blastn process. original script: scripts/07_annotation_modified.sh original command: blastn -num_threads ${threads} -db ${db}/${rrna} -query ${f}.fna -out ${f}_${rrna}.txt -outfmt \"6 qseqid sseqid stitle evalue\" -max_target_seqs 1 -evalue 0.1\"
BLASTN_rRNA_alignment_silva_138.1_SSUParc_tax_silva	../Tools/10_blastn_rRNA_alignment.cwl (CommandLineTool)	blastn command for rRNA database creation	\"This tool is used to execute blastn process. original script: scripts/07_annotation_modified.sh original command: blastn -num_threads ${threads} -db ${db}/${rrna} -query ${f}.fna -out ${f}_${rrna}.txt -outfmt \"6 qseqid sseqid stitle evalue\" -max_target_seqs 1 -evalue 0.1\"

Outputs

ID	Type	Label	Doc
BLASTN_rRNA_concat_file	File	blastn result file	blastn result file
FILTERED_rRNA_PROTEIN_FASTA_FILE	File	filtered rRNA protein fasta file	filtered rRNA protein fasta file

Permalink: https://w3id.org/cwl/view/git/1838569c1d6d3c15f58c254667d4c6258e67e5a6/Workflow/blastn_rRNA_ssw.cwl