CWL Workflow: RNASelector as a CWL workflow

Workflow: RNASelector as a CWL workflow

Fetched 2023-01-09 07:25:37 GMT

Verified with cwltool version 3.1.20221201130942

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

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.

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

ID	Runs	Label	Doc
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	../tools/rRNA_selection.cwl (Workflow)
find_16S_matches	../tools/rRNA_selection.cwl (Workflow)
find_23S_matches	../tools/rRNA_selection.cwl (Workflow)
find_tRNA_matches	../tools/tRNA_selection.cwl (Workflow)
mask_rRNA_and_tRNA	../tools/mask_RNA.cwl (CommandLineTool)
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	../tools/collate_unique_SSU_headers.cwl (Workflow)
collate_unique_tRNA_hmmer_hits	../tools/collate_unique_SSU_headers.cwl (Workflow)

ID	Type	Label	Doc
5S_matches	File [FASTA]
16S_matches	File [FASTA]
23S_matches	File [FASTA]
tRNA_matches	File [FASTA]
masked_sequences	File [FASTA]