qc_report will only take full path to zipfiles

[ACharbonneau]

I'm running fastqrc from the folder that contains all the zip files.

qc.path <- "."

Running list.files(qc.path) gives files as expected, and qc <- qc_aggregate(qc.path) gives a valid report, however qc_report(qc.path, result.file = "test") gives:

Quitting from lines 51-53 (multi-qc-report.Rmd)
Error in qc_aggregate(qc.path, progressbar = FALSE) :
Can't find any *fastqc.zip files in the specified qc.dir

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

[kassambara]

Hi,

Thank you for pointing this out.

The following code should work:

qc_report(qc.path = getwd(), result.file = "test")

[kassambara]

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")

[ACharbonneau]

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!

[kassambara]

oh, great! so we can close this issue. Thank you again for pointing this out.

[kassambara]

better stable solution to handle relative path added now