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tgirke / systemPipeR

Project Website:
http://girke.bioinformatics.ucr.edu/systemPipeR
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Construct SYSargs2 object from CWl param, CWL input, and targets files #18

Closed cbiOPela closed 5 years ago

cbiOPela commented 5 years ago

Hi all!

Congrats for your fantastic package!

I'am trying to use your tool with my own data following your recommendations. I get this error in the step specified in the title. Until renderWF everything is OK. My question is: what is needed by renderWF in inputvars (FileName and SampleName)

I paste last lines of the code i'm running

dir_path <- paste0(getwd(),"/param/cwl/preprocessReads/trim-se") dir_path trim <- loadWorkflow(targets = targetspath, wf_file = "trim-se.cwl", input_file = "trim-se.yml", dir_path = dir_path)

trim <- renderWF(trim, inputvars=c(FileName="data/SRR1016916", SampleName="M1A"))

And the error printed:

Error in if (basecommand[1] == "mkdir") { : argument is of length zero

Thank you in advance!!

dcassol commented 5 years ago

Hi @cbiOPela, Thank you for using systemPipeR!

Could you please provide the output of sessionInfo() executed in an R session right after the error occurred?

Also, note that in the argument inputvars, the variable names defined in the trim.yml as _FASTQ_PATH1_ and _SampleName_, need to match the column names defined in the targets file (in your case, targetspath). It is possible to assign NULL in the targets argument (loadWorkflow function) to run the pipeline without 'targets' file. This case can be useful for running a specific command-line tool, which does not require different input files (for example, when we create the index for the alignment).

dcassol commented 5 years ago

Hello @cbiOPela, I'm going to close this for now, as we haven't heard back from you in a while. Feel free to re-open if you have any additional questions. Cheers,