Workflow: preprocess fasta
Fetched 2023-01-12 19:59:28 GMT
Verified with cwltool version 3.1.20221201130942
Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| jobid | String | ||
| stats | File | ||
| filterLn | Boolean | ||
| maxAmbig | Integer | ||
| deviation | Float | ||
| sequences | File | ||
| filterAmbig | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter |
../Tools/filter_fasta.tool.cwl
(CommandLineTool)
|
filter fasta |
filter fasta file based on sequence length and/or on number of ambiguity characters (Ns) skipping both filters is equivalent to copying the file, but slower |
| adapterTrim |
../Tools/autoskewer.tool.cwl
(CommandLineTool)
|
autoskewer |
detect and trim adapter sequences from reads >autoskewer.py -t <runtime.tmpdir> -i <input> -o <outName> -l <outLog> |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| passed | File | ||
| removed | File | ||
| trimmed | File |
Permalink:
https://w3id.org/cwl/view/git/4e4d2e674bde612f98f2b0370445f8b2a47587df/CWL/Workflows/preprocess-fasta.workflow.cwl
