Workflow: A workflow that aligns a fasta file and provides statistics on the SAM file
Fetched 2024-11-21 10:41:54 GMT
Verified with cwltool version 3.1.20230201224320
A workflow that aligns a fasta file and provides statistics on the SAM file
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bwa_opt | String | ||
| ref_fasta | File | ||
| read1_fastq | File | ||
| read2_fastq | File | ||
| sample_name | String | ||
| ref_fasta_sa | File | ||
| ref_fasta_amb | File | ||
| ref_fasta_ann | File | ||
| ref_fasta_bwt | File | ||
| ref_fasta_fai | File | ||
| ref_fasta_pac | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| flagstat |
9eefcdcc93bbee2e33b21626cbd4f96b
(CommandLineTool)
|
||
| bwa_align |
946d1ff97fbee015e65bc4c8954c82d1
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_sam | File | ||
| output_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/81526c069d76fccb06202140512011481232c999/cwl-training/exercise3/solution/align_and_metrics.cwl
