# GAlign
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_GAlign.R (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| fastq1 | string | ||
| fastq2 | string | ||
| readGroup | string | ||
| sampleName | string | ||
| library | string | ||
| platunit | string | ||
| platform | string | ||
| center | string | ||
| tmpl1 | File | ||
| wdl1 | File | ||
| tmpl2 | File | ||
| wdl2 | File | ||
| cromwell | File |
# Outputs
| label | type | description | |
|---|---|---|---|
| bamlog | File | ||
| outdir | Directory |
# steps
| label | doc | |
|---|---|---|
| fqJson | ||
| fq2ubam | ||
| ubam2bamJson | ||
| align | ||
| mvOut |