Custom protocol patch #42
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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.
ewels
requested changes
Jul 3, 2020
main.nf
Outdated
| @@ -722,7 +723,7 @@ process mirtrace { | |||
| mirtrace qc \\ | |||
| --species $params.mirtrace_species \\ | |||
| $primer \\ | |||
| --protocol $protocol \\ | |||
| $protocol_opt $protocol \\ | |||
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Suggested change
| $protocol_opt $protocol \\ | |
| $protocol_opt \\ |
I think that the current code will output the protocol name twice..
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Resolved within fixing the merge conflicts
6 tasks
|
Merging despite failing tests so that I can bring this change into #55 |
ewels
added a commit
to ewels/nf-core-smrnaseq
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Nov 7, 2020
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Implemented a fix for issue 41, where
--protocol customwasn't being accepted. This was due to miRtrace not having a defined argument for custom, which caused it to error out.Also added some documentation to make it clearer that there is a custom option for users to define their own adapter and trimming parameters if required.