Workflow: pipeline-fastq2vcf-multisample.cwl
DNAseq pipeline from fastq to vcf for multiple samples
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
dbsnp | File (Optional) | ||
sample | String[] | ||
library | String[] | ||
threads | Integer (Optional) | ||
interval | File (Optional) | ||
platform | String (Optional) | ||
readgroup | String[] | ||
reference | File | ||
chunk_size | Integer (Optional) | ||
input_reads | 795a8873042f7a6fbfe26969d98de71a[] | ||
mark_secondary | Boolean (Optional) | ||
bqsr_known_sites | File[] | ||
realign_known_sites | File[] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
pipeline |
pipeline-fastq2vcf.cwl
(Workflow)
|
DNAseq pipeline from fastq to vcf |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
output | File[] | ||
bwa_output | File[] | ||
qcal_output | File[] | ||
dedup_output | File[] | ||
realign_output | File[] | ||
qcal_plot_output | File[] (Optional) | ||
dedup_metric_output | File[] (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/pipeline/pipeline-fastq2vcf-multisample.cwl