The goal of BioC19CWL is to ...
A python package cwltool is required to be installed. The cwltool is the reference implementation of the Common Workflow Language, which is used to run the CWL scripts. Here is the instruction to install the tool. https://github.com/common-workflow-language/cwltool#install
The Docker engine requirement is optional, but it can simplify software installation and management.
Hisat2 is required to be installed.
> library(RcwlPipelines)
Loading required package: BiocFileCache
Loading required package: dbplyr
> input1 <- InputParam(id = "sth")
> echo <- cwlParam(baseCommand = "echo", inputs = InputParamList(input1))
> echo$sth <- "Hello World!"
> echo
class: cwlParam
cwlClass: CommandLineTool
cwlVersion: v1.0
baseCommand: echo
inputs:
sth (string): Hello World!
outputs:
output:
type: stdout
r1 <- runCWL(echo, outdir = tempdir())
r1
> r1 <- runCWL(echo, outdir = tempdir())
INFO Final process status is success
Error in idx[1]:(idx[2] - 1) : NA/NaN argument
This looks like a bug? If you could take a quick look, that would be great, as we are trying to finalize the AMI. Thanks!
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