custom aligner option disappeared in v1.5.0

[Flowdihow]

Hi Jin,

it seems that the custom aligner/peak options have disappeared in the last two releases. May I ask, why this is the case?

We are investigating to which extend the pipeline can be used for other technologies as well (such as CUT&RUN). In this respect, we would like to try different bowtie parameters. Is there a chance to achieve this?

Thank you very much
Best,
Florian

[akundaje]

This should be supported. @jin - can you reactivate this and update the documentation. Thanks

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On Thu, Jul 2, 2020, 5:32 AM Flowdihow ***@***.***> wrote: Hi Jin, it seems that the custom aligner/peak options have disappeared in the last two releases. May I ask, why this is the case? We are investigating to which extend the pipeline can be used for other technologies as well (such as CUT&RUN). In this respect, we would like to try different bowtie parameters. Is there a chance to achieve this? Thank you very much Best, Florian — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#170>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDWEJCGUIIPZSFMXTHUSTRZR45PANCNFSM4OO26WPA> .

[Flowdihow]

Hi Yin & Anshul,

Thanks for your support!

Best,
Flo

[leepc12]

Could you please check if this WDL on branch PIP-1287_reenable_custom_aligner works with your custom aligner?
Added custom_align_py and custom_aligner_idx_tar back to the code.

[Flowdihow]

Hi Yin,

sorry for coming back to you so late. Everything works fine as expected!

Thanks Flo