Workflow: CGC-subwf.cwl
Fetched 2024-05-19 12:46:41 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| maskfile | File | ||
| fgs_train | String | ||
| postfixes | String[] | ||
| chunk_size | Integer | ||
| input_fasta | File | ||
| genecaller_order | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| combine |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/concatenate.cwl
(CommandLineTool)
|
Redirecting Multiple Files Contain in a Single File |
The cat (short for concatenate) command is one of the most frequently used command in Linux/Unix like operating systems. cat command allows us to create single or multiple files, view contain of file, concatenate files and redirect output in terminal or files. |
| count_cds |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/utils/count_fasta.cwl
(CommandLineTool)
|
||
| split_seqs |
/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/tools/chunks/dna_chunker/fasta_chunker.cwl
(CommandLineTool)
|
split FASTA by number of records |
based upon code by Maxim Scheremetjew, EMBL-EBI |
| combined_gene_caller |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| results | File[] [FASTA] | ||
| count_faa | Integer |
Permalink:
https://w3id.org/cwl/view/git/a83ee883bb3c7480010fa952939fac771491ddf4/workflows/subworkflows/assembly/CGC-subwf.cwl
