Workflow: extract other ncrnas!

Fetched 2024-05-20 18:47:36 GMT
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Inputs

ID Type Title Doc
name_string String
cmsearch_file File
input_sequences File
other_ncRNA_ribosomal_models String[]

Steps

ID Runs Label Doc
get_coords
../../tools/RNA_prediction/pull_ncrnas/pull_ncrnas.cwl (CommandLineTool)
get_ncrnas
../../tools/RNA_prediction/easel/esl-sfetch-manyseqs.cwl (CommandLineTool)
extract by names from an indexed sequence file

https://github.com/EddyRivasLab/easel
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
rename_ncrnas
../../utils/move.cwl (CommandLineTool)
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.

Outputs

ID Type Label Doc
ncrnas File[]
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/workflows/subworkflows/other_ncrnas.cwl