Workflow: Creates FASTA file from BED coordinates
Fetched 2023-10-22 20:54:20 GMT
Verified with cwltool version 3.1.20230201224320
This workflow creates FASTA file from BED coordinates
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/ncbi/cwl-ngs-workflows-cbb/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bed | File | ||
| fasta | File | ||
| fasta_out | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort |
../../tools/basic/sort.cwl
(CommandLineTool)
|
sort |
SORT command |
| bedtocoord |
../../tools/basic/awk.cwl
(CommandLineTool)
|
awk |
AWK command |
| samtools_faidx |
../../tools/samtools/samtools-faidx.cwl
(CommandLineTool)
|
Samtools-faidx |
Samtools is a suite of programs for interacting with high-throughput sequencing data |
| remove_comments |
../../tools/basic/grep.cwl
(CommandLineTool)
|
grep |
GREP command |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File |
Permalink:
https://w3id.org/cwl/view/git/1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49/workflows/File-formats/fasta-from-bed.cwl
