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gkno / gkno_launcher

The gkno launcher for executing tools or pipelines
MIT License
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Wildcard #51

Closed AlistairNWard closed 9 years ago

AlistairNWard commented 9 years ago

Consider the following example:

gkno bwa -q _1.fq -q2 _2.fq

The wildcards will be evaluated by bash and fed to gkno, however the order in which the lists appear cannot be guaranteed. For this to work, each X_1.fq must be paired with the correct X_2.fq. Either include logic in configuration file instructing gkno to look for shared patterns, or provide a general check. If multiple arguments are given multiple values on the command line, check to see if there is any common text between the values and order accordingly.

AlistairNWard commented 9 years ago

Tool configuration files can include the 'linked argument' field in the arguments section. If arguments are linked, the values are reordered to achieve maximum similarity between corresponding elements of linked arguments value lists. If lists are reordered, the user is warned. This feature can be disabled with the --do-not-reorder (-dnr) flag.