Workflow: rRNA_selection.cwl
Fetched 2023-01-09 04:19:19 GMT
Verified with cwltool version 3.1.20221201130942
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- |
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- Inputs/Outputs
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 |
|---|---|---|---|
| model | File [HMMER format] | rRNA protein model to search with | |
| indexed_sequences | File [FASTA] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| hmmsearch |
hmmsearch.cwl
(CommandLineTool)
|
search profile(s) against a sequence database | |
| sort_matches |
RevReadSort.cwl
(CommandLineTool)
|
||
| reformat_matches |
oneLineFasta.cwl
(CommandLineTool)
|
reformats FASTA. single line sequence, adds 'length=' to header drops seqs with identical IDs (up until the first `/`) |
|
| extract_coord_lines |
extract_coord_lines.cwl
(CommandLineTool)
|
||
| extract_coordinates |
rRNA_selection.cwl#extract_coordinates/extract_coordinates
(CommandLineTool)
|
||
| fetch_aligned_sequences |
esl-sfetch-manyseqs.cwl
(CommandLineTool)
|
extract by names from an indexed sequence file |
https://github.com/EddyRivasLab/easel |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| matching_sequences | File [FASTA] | ||
| hmmer_search_results | File |
Permalink:
https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/rRNA_selection.cwl
