custom protocol implementation #1
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A quick patch to fix the handling of --protocol (specifically custom) options when passing off to miRtrace.
Amended documentation around `--protocol` to better reflect that the user can use a custom protocol and provide their own adapter and trimming parameters.
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A quick patch to fix the handling of --protocol (specifically custom) options when passing off to miRtrace. This fix was discussed and decided upon in this issue.
Briefly, when working with 'custom' adapters (i.e.
--protocol custom) the pipeline would fail. This was due to miRtrace not recognisingcustomas a valid option to--protocol. The proposed fix addresses this issue.