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Hi all, I'm currently using the dev version to pro...
# genomeassembler
u
Hi all, I'm currently using the dev version to process a new genome and hit an issue with a very large contig after RagTag, which causes .bai indexing to fail... To workaround it I completely replaced bai indexes with csi indexes and am happy as rain... Two questions. 1) Is there already an easy way I didn't spot to use CSI indexes with the pipeline? 2) If not, is there any reason why we can't change the CSI to be default? Happy to submit a PR if anyone thinks it is useful.
n
Hi, I never encountered this issue, so thanks for reporting. I think should rather straightforward, essentially adding something like this in a config:
Copy code
withName: '.*SAMTOOLS:INDEX.*' { ext.args = "-c" }
While I think this is an easy way, it may not be extremely obvious for users 😉 so maybe adding a param that switches that would be a good idea.
but I think this may not properly pass the 
csi
file to whatever comes next, so I see that this is not a good solutoin
Feel free to submit a PR if you already figured out which places this needs to ba changed
I think it would generally be better to switch to 
csi
throughout, it seems like 
bai
has no advantages
u
Thanks, will do the PR over the next week. I see no reason why it won't pass the linting tests, but I will check it as suggested in the PR template.
n
Ok, the main reason why you should check if it passes linting, is that the PR will be linted as part of CI and if it fails, you will have to fix linting or we cannot merge..
https://github.com/nf-core/genomeassembler/pull/171/commits/7e1846204765cb989d0541a1340a5d784c7356ba Please let me know if this is in line with what you have put into a PR
u
n
Ok, I will compare. Thanks
u
I can still submit a PR, probably tomorrow morning if any easier
n
Yeah, that would probably help, thanks
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