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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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setupFileCreator return code is 0 even if it fails #35

Closed mariogiov closed 9 years ago

mariogiov commented 9 years ago

This specific error is actually just because I forgot to update PIper on Nestor but the return code problem I think is probably still an issue? It would be handy to fix this because if this step fails it would be good for the Python script calling it to know:

ipdb> print(stderr)
Error: Unknown option --qos
Error: Unknown argument 'seqver'
SetupFileCreator  - A utility program to create pipeline setup xml files for Piper..
Usage: SetupFileCreator [options]

  -o Output xml file. | --output Output xml file.
        This is a required argument.
  -p The name of this project. | --project_name The name of this project.
        This is a required argument.
  -s The technology used for sequencing, e.g. Illumina | --sequencing_platform The technology used for sequencing, e.g. Illumina
        This is a required argument.
  -c Where the sequencing was carried out, e.g. NGI | --sequencing_center Where the sequencing was carried out, e.g. NGI
        This is a required argument.
  -a The uppnex project id to charge the core hours to. | --uppnex_project_id The uppnex project id to charge the core hours to.
        This is a required argument.
  -i Input path to fastq files to include in analysis. | --input_fastq Input path to fastq files to include in analysis.
        This is a required argument. Can be specified multiple times.
  -r Reference fasta file to use. | --reference Reference fasta file to use.
        This is a required argument.

ipdb> p_h.returncode 
0
johandahlberg commented 9 years ago

You are right. I can confirm this in the code. How soon do you need a fix?

mariogiov commented 9 years ago

No rush, I can just check if the return text is in stderr or stdout for the moment, but I always just feel better about checking return codes..

On Nov 10, 2014, at 13:35, Johan Dahlberg notifications@github.com wrote:

You are right. I can confirm this in the code. How soon do you need a fix?

— Reply to this email directly or view it on GitHub https://github.com/NationalGenomicsInfrastructure/piper/issues/35#issuecomment-62378350.

johandahlberg commented 9 years ago

I'll put this on the todo list.