fix cutadapt paired untrimmed command #423
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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. |
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Tests passing, many thanks! |
sebastian-luna-valero
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sebastian-luna-valero
added a commit
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that referenced
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May 31, 2018
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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)