Workflow: lobSTR-workflow.cwl
Fetched 2024-04-25 05:59:32 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
Requires:
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 |
|---|---|---|---|
| p1 | File[] (Optional) |
list of files containing the first end of paired end reads in fasta or fastq format |
|
| p2 | File[] (Optional) |
list of files containing the second end of paired end reads in fasta or fastq format |
|
| rg-lib | String |
Use this in the read group LB tag |
|
| strinfo | File |
File containing statistics for each STR. |
|
| reference | File |
lobSTR's bwa reference files |
|
| rg-sample | String |
Use this in the read group SM tag |
|
| noise_model | File |
File to read noise model parameters from (.stepmodel) |
|
| output_prefix | String |
prefix for output files. will output prefix.aligned.bam and prefix.aligned.stats |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| lobSTR |
lobSTR-tool.cwl
(CommandLineTool)
|
lobSTR |
lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data. |
| samsort |
samtools-sort.cwl
(CommandLineTool)
|
Invoke 'samtools sort' (samtools 1.19) |
|
| samindex |
samtools-index.cwl
(CommandLineTool)
|
Invoke 'samtools index' to create a 'BAI' index (samtools 1.19) |
|
| allelotype |
allelotype.cwl
(CommandLineTool)
|
Run lobSTR allelotype classifier. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| vcf | File | ||
| bam_stats | File | ||
| vcf_stats | File |
Permalink:
https://w3id.org/cwl/view/git/767d700e602805112a4c953d166e570cddfa2605/workflows/lobSTR/lobSTR-workflow.cwl
