Workflow: RNASelector as a CWL workflow

Fetched 2019-12-06 21:08:11 GMT

https://doi.org/10.1007/s12275-011-1213-z

children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
run_id String
23S_model File [HMMER format]
16S_model File [HMMER format]
tRNA_model File [HMMER format]
reads File [FASTA]
5S_model File [HMMER format]

Steps

ID Runs Label Doc
mask_rRNA_and_tRNA
../tools/mask_RNA.cwl (CommandLineTool)
find_tRNA_matches
prepend_header_for_QIIME
../tools/prepend_header.cwl (CommandLineTool)
prepend a string + an underscore to all headers in a FASTA sequence file
collate_unique_rRNA_hmmer_hits
find_16S_matches
index_reads
../tools/esl-sfetch-index.cwl (CommandLineTool)
index a sequence file for use by esl-sfetch

https://github.com/EddyRivasLab/easel

find_5S_matches
find_23S_matches
collate_unique_tRNA_hmmer_hits

Outputs

ID Type Label Doc
16S_matches File
5S_matches File
masked_sequences File
tRNA_matches File
23S_matches File
Permalink: https://w3id.org/cwl/view/git/c2110714be230861ee7b96adc3db6e32e5248c57/workflows/rna-selector.cwl