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CGATOxford / CGATPipelines

Collection of CGAT NGS Pipelines
MIT License
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fix cutadapt paired untrimmed command #423

Closed amayer21 closed 6 years ago

amayer21 commented 6 years ago

When running cutadapt (from readqc pipeline) with paired reads and asking to redirect untrimmed reads to a separate file, there are spaces missing in the command before --untrimmed-output so the run abort with an error message. Also the option for redirecting untrimmed paired output should be --untrimmed-paired-output and not --untrimmed-output-paired.

Both problem fixed here (both coming from same line in PipelinePreprocess.py)

Acribbs commented 6 years ago

These changes look good to me. I think the reason we don't pick this up is that we don't have tests to capture running cutadapt.

When we have finished the refactoring of the cgat-developer repository maybe its something we can look at making tests for this.

sebastian-luna-valero commented 6 years ago

Tests passing, many thanks!