Fix submit command in error message for grid executors that pipe wrapper script #3548
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…wrapper script Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Added unit test 👍 |
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…per script (nextflow-io#3548) Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Closes #3024
Some grid executors pipe the wrapper script to their submit command (e.g. LSF). In this case, when a task fails and Nextflow prints an error message, the submit command is incorrect because it doesn't include the pipe. For example:
The submit command in this case should be
bsub < .command.run.This PR changes the error message to append
< .command.runto the command if the wrapper script was piped into the submit command.