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gkno / gkno_launcher

The gkno launcher for executing tools or pipelines
MIT License
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Output files #45

Closed AlistairNWard closed 9 years ago

AlistairNWard commented 9 years ago

Check that the number of output files is equal to the number of inputs. If n files are supplied to a non-greedy task, the task will be run n times generating n outputs. If n inputs are supplied on the command line and m outputs are supplied, there will be a problem! Ensure that this is handled.

AlistairNWard commented 9 years ago

Checks for outputs are complete, but an additional check is required. Consider a variant calling pipeline where a single bam file is provided, but multiple reference fasta files. In this case, the task needs to be run multiple times, once for each reference sequence. The output files are constructed using the input bam file name, so the number of output files created will be one causing a problem. Catch this problem and prompt the user to explicitly specify the output filenames or update the filename construction instructions.