setupFileCreator return code is 0 even if it fails
mariogiov opened this issue · comments
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
You are right. I can confirm this in the code. How soon do you need a fix?
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 #35 (comment).
I'll put this on the todo list.