Workflow: Identifies non-coding RNAs using Rfams covariance models

Fetched 2019-11-20 22:29:20 GMT
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Inputs

ID Type Title Doc
cores Integer
clan_info File
query_sequences File
covariance_models File[]

Steps

ID Runs Label Doc
remove_overlaps
../tools/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.cwl (CommandLineTool)
Remove lower scoring overlaps from cmsearch --tblout files.

https://github.com/nawrockie/cmsearch_tblout_deoverlap/blob/master/00README.txt

cmsearch
../tools/Infernal/cmsearch/infernal-cmsearch-v1.1.2.cwl (CommandLineTool)
Search sequence(s) against a covariance model database

Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. Please visit http://eddylab.org/infernal/ for full documentation. Version 1.1.2 can be downloaded from http://eddylab.org/infernal/infernal-1.1.2.tar.gz

concatenate_matches
../utils/concatenate.cwl (CommandLineTool)
Redirecting Multiple Files Contain in a Single File

The cat (short for “concatenate“) command is one of the most frequently used command in Linux/Unix like operating systems. cat command allows us to create single or multiple files, view contain of file, concatenate files and redirect output in terminal or files.

Outputs

ID Type Label Doc
deoverlapped_matches File
Permalink: https://w3id.org/cwl/view/git/72f702591368397f56d455128f60916902104dd2/workflows/cmsearch-multimodel-wf.cwl