Fix URIs matching error in sdrfToNfConf.R

[pmb59]

The PR fixes the error for the droplet protocol, that arises when uri_select is not a matrix or a data.frame:

During startup - Warning message:
Setting LC_CTYPE failed, using "C"
Error in FUN(X[[i]], ...) :
  Can't find URIs matching files: SRR13491863_2.fastq.gz
Calls: lapply -> FUN -> lapply -> FUN
Execution halted

The PR now reports a single value (TRUE or FALSE) as expected, as files in this case

          } else {
            missing_uri_files <- files[which(! any(apply(species.protocol.sdrf[, uri_cols], 2, function(x) basename(x) == files))  )]

has a single file.

Tested with the following accessions: E-GEOD-153723, E-GEOD-157775, E-MTAB-4850

[anilthanki]

Can you please explain briefly what are you trying to do here.. So I know what I understood from code is right..

[pmb59]

Hi @anilthanki Did you have a look to the description of the PR?

Basically, in this chunk for each library it is checked if there is a fastq URI that can supply the file. The error was in the fix for the case when uri_select is not a matrix or a data.frame

[anilthanki]

LGTM

[pmb59]

Thanks for reviewing @anilthanki