Workflow: RD_Connect
Fetched 2024-05-06 14:30:25 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| gqb | Integer[] |
Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) |
|
| chromosome | String |
Label of the chromosome to be used for the analysis. By default all the chromosomes are used |
|
| fastq_files | File[] |
List of paired-end input FASTQ files |
|
| sample_name | String |
Sample name |
|
| readgroup_str | String |
Parsing header which should correlate to FASTQ files |
|
| known_sites_file | File |
VCF file correlated to reference genome assembly with know sites (for instance dbSNP) |
|
| reference_genome | File[] |
Compress FASTA files with the reference genome chromosomes |
|
| known_indels_file | File |
VCF file correlated to reference genome assembly with known indels |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gunzip |
../tools/gunzip.cwl
(CommandLineTool)
|
||
| bwa_mem |
../tools/bwa-mem.cwl
(CommandLineTool)
|
||
| bwa_index |
../tools/bwa-index.cwl
(CommandLineTool)
|
||
| unzipped_known_sites |
../tools/gunzip_known_sites.cwl
(CommandLineTool)
|
||
| unzipped_known_indels |
../tools/gunzip_known_sites.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File |
unannotated gVCF output file from the mapping and variant calling pipeline |
|
| metrics | File |
Several metrics about the result |
Permalink:
https://w3id.org/cwl/view/git/31348ed533961f84cf348bf1af660ad9de6f870c/cwl-workflows/workflows/workflow.cwl
