Workflow: preprocessing.cwl
Fetched 2024-12-10 08:34:25 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File | ||
| threads | Integer | ||
| coverage | Integer | ||
| genome_size | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastp |
../tool/fastp/fastp.cwl
(CommandLineTool)
|
||
| fastqc_raw |
../tool/fastqc/fastqc-PE.cwl
(CommandLineTool)
|
||
| calc_proportion |
../tool/dfast-utility/util_calc_proportion.cwl
(CommandLineTool)
|
||
| seqkit_stats_raw |
../tool/seqkit/seqkit-stats-PE.cwl
(CommandLineTool)
|
||
| fastqc_subsampled |
../tool/fastqc/fastqc-PE.cwl
(CommandLineTool)
|
||
| seqkit_subsample1 |
../tool/seqkit/seqkit-sample.cwl
(CommandLineTool)
|
||
| seqkit_subsample2 |
../tool/seqkit/seqkit-sample.cwl
(CommandLineTool)
|
||
| seqkit_stats_fastp |
../tool/seqkit/seqkit-stats-PE.cwl
(CommandLineTool)
|
||
| seqkit_stats_subsample |
../tool/seqkit/seqkit-stats-PE.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastp_fastq1 | File | ||
| fastp_fastq2 | File | ||
| read-stats_raw | File | ||
| read-stats_fastp | File | ||
| subsampled_fastq1 | File | ||
| subsampled_fastq2 | File | ||
| fastqc_result_raw1 | File | ||
| fastqc_result_raw2 | File | ||
| read-stats_subsample | File | ||
| fastqc_result_subsampled1 | File | ||
| fastqc_result_subsampled2 | File |
Permalink:
https://w3id.org/cwl/view/git/d0d36f70eb62164d57c1ba27a6b63bee7d41e370/cwl/workflow/preprocessing.cwl
