add ignore_soft_clipped_bases option

[pcantalupo]

nf-core/sarek pull request

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[maxulysse]

Hi @pcantalupo, Thanks a lot for your PR.
I have a couple issues.
It seems that you made it from the master branch instead of the dev branch.
I changed the target branch to dev and we now have way more modifications that we should have.
I'll suggest you to follow our contributing guidelines.

[maxulysse]

Hi @pcantalupo thanks again for this first PR.

• Can you add this params with the default value null in nextflow.config somewhere along https://github.com/nf-core/sarek/blob/dev/nextflow.config#L68

• I'm not sure about the params name. dont_use_soft_clipped_bases seems to long to me, but I do understand the idea behind copying the params name from Mutect2.
  @szilvajuhos @ggabernet @apeltzer @FriederikeHanssen any ideas or opinion on that matter?

[drpatelh]

--ignore_soft_clipped_bases is better I think. Could use --ignore_soft_clipped too but that may lead to confusion with reads that are soft-clipped and not the bases themselves.

[maxulysse]

@pcantalupo if you agree with the suggestions we propose, you can batch accept them if you're in the files changes tab.
That way you can do only one commit directly here on github

[maxulysse]

Thanks a lot @pcantalupo for this first PR