Workflow: preprocess fasta
Fetched 2024-11-13 03:38:51 GMT
Verified with cwltool version 3.1.20230201224320
Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.
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- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
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/932da3abed7166bd5a962871386ba2c31d47b85c/CWL/Workflows/preprocess-fasta.workflow.cwl
