CWL Workflow: rna_prediction-sub-wf.cwl

Workflow: rna_prediction-sub-wf.cwl

Fetched 2024-05-20 20:30:11 GMT

Verified with cwltool version 3.1.20230201224320

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

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

Inputs

ID	Type	Title	Doc
type	String
pattern_5S	String
pattern_LSU	String
pattern_SSU	String
pattern_5.8S	String
silva_lsu_otus	String
silva_ssu_otus	String
input_sequences	File
silva_lsu_database	File
silva_lsu_taxonomy	String
silva_ssu_database	File
silva_ssu_taxonomy	String
ncRNA_ribosomal_models	String[]
ncRNA_ribosomal_model_clans	String

Steps

ID	Runs	Label	Doc
gzip_files	../../utils/pigz/gzip.cwl (CommandLineTool)
index_reads	../../tools/RNA_prediction/easel/esl-sfetch-index.cwl (CommandLineTool)	index a sequence file for use by esl-sfetch	https://github.com/EddyRivasLab/easel
classify_LSUs	classify-otu-visualise.cwl (Workflow)	Run taxonomic classification, create OTU table and krona visualisation
classify_SSUs	classify-otu-visualise.cwl (Workflow)	Run taxonomic classification, create OTU table and krona visualisation
extract_coords	../../tools/RNA_prediction/extract-coords/extract-coords_awk.cwl (CommandLineTool)		The awk script takes the output of Infernal's cmsearch so-called fmt=1 mode and makes it suitable for use by esl-sfetch, a sequence selector Reading the user's guide for Infernal, Version 1.1.2; July 2016 http://eddylab.org/infernal/Userguide.pdf#page=60 we see that the relevant fields in the cmsearch output are: (column number: explanation) 1: The name of the target sequence or profile 3: The name of the query sequence or profile 8: The start of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues. 9: The end of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues Likewise the format esl-sfetch wants is: <newname> <from> <to> <source seqname> Putting it all together we see that the newname (which esl-sfetch with output using) is a concatenation of the original name, the sequence number, and the coordinates.
count_lsu_fasta	../../utils/count_fasta.cwl (CommandLineTool)
count_ssu_fasta	../../utils/count_fasta.cwl (CommandLineTool)
extract_subunits	../../tools/RNA_prediction/get_subunits_fasta/get_subunits.cwl (CommandLineTool)
extract_sequences	../../tools/RNA_prediction/easel/esl-sfetch-manyseqs.cwl (CommandLineTool)	extract by names from an indexed sequence file	https://github.com/EddyRivasLab/easel
find_ribosomal_ncRNAs	cmsearch-condition.cwl (Workflow)	Identifies non-coding RNAs using Rfams covariance models
extract_subunits_coords	../../tools/RNA_prediction/get_subunits_coords/get_subunits_coords.cwl (CommandLineTool)

Outputs

ID	Type	Label	Doc
ncRNA	File
LSU_fasta	File (Optional)
SSU_fasta	File (Optional)
LSU_coords	File
LSU_folder	Directory (Optional)
SSU_coords	File
SSU_folder	Directory (Optional)
LSU-SSU-count	File
cmsearch_result	File
compressed_rnas	File[]
number_LSU_mapseq	Integer
number_SSU_mapseq	Integer

Permalink: https://w3id.org/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/workflows/subworkflows/rna_prediction-sub-wf.cwl