Closed ACharbonneau closed 7 years ago
Hi,
Thank you for pointing this out.
The following code should work:
qc_report(qc.path = getwd(), result.file = "test")
fixed now! Please, install the latest developmental version and let me know if it works now when using qc.path = "." .
To install:
if(!require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/fastqcr")
Beat me to it. But it doesn't like the getwd solution:
qc_report(qc.path = getwd(), result.file = "test") Error in qc_report(qc.path = getwd(), result.file = "test") : unused arguments (qc.path = getwd(), result.file = "test")
Developer version works great though. Thanks!
oh, great! so we can close this issue. Thank you again for pointing this out.
better stable solution to handle relative path added now
I'm running fastqrc from the folder that contains all the zip files.
Running
list.files(qc.path)
gives files as expected, andqc <- qc_aggregate(qc.path)
gives a valid report, howeverqc_report(qc.path, result.file = "test")
gives:Replacing the relative path with a full path to the same directory allows both qc_aggregate and qc_report to run, but requiring full paths limits the program's usability for scripting. This is on an HPC, running R/3.2.0 and pandoc/1.17.3