Is there a situation in which the ref is actually ...
# moduless
Sam Wilkinson
10/02/2025, 9:30 AMIs there a situation in which the ref is actually required for samtools coverage? https://github.com/nf-core/modules/blob/master/modules/nf-core/samtools/coverage/main.nf
As far as I can tell this samtools command never makes use of the ref argument
✅ 1
m
Matthias De Smet
10/02/2025, 9:41 AMCram input?
s
Sam Wilkinson
10/02/2025, 9:43 AMSurely cram stores all the necessary info about the ref for coverage, all it needs is ref name, length, and alignment positions
Sam Wilkinson
10/02/2025, 9:43 AMbut that could be it I guess
Sam Wilkinson
10/02/2025, 9:44 AMreference isn't even listed as an arg here: https://www.htslib.org/doc/samtools-coverage.html
Sam Wilkinson
10/02/2025, 9:45 AMso I'm convinced it's vestigial
m
Matthias De Smet
10/02/2025, 10:02 AMthe
--references
Sam Wilkinson
10/02/2025, 10:04 AMit is, but that doesn't mean it actually does anything within this context
m
Matthias De Smet
10/02/2025, 10:06 AMThat’s true. In this case I’d say test it and report back, then we can ditch the output if needed.
Or just ignore it 🤷🏻
SAMTOOLS_COVERAGE(input, [[:],[]],[[:],[]])s
Sam Wilkinson
10/02/2025, 10:07 AMYeah I was going to do a PR but wanted to check I wasn't missing anything obvious
Sam Wilkinson
10/02/2025, 10:07 AMit actually breaks if you don't provide it in this case 🙂
Sam Wilkinson
10/02/2025, 10:07 AMsince
--referenceSam Wilkinson
10/02/2025, 10:08 AMlike
Copy code
reference = fastq ? "--reference ${fasta}" : ""m
Matthias De Smet
10/02/2025, 10:08 AMYeah, I’m to blame for that one 😅
https://github.com/nf-core/modules/commit/38afbe42f7db7f19c7a89607c0a71c68f3be3131
🙃 1
s
Sam Wilkinson
10/02/2025, 10:09 AMit happens, easily done
Sam Wilkinson
10/02/2025, 10:13 AMoh ffs you are right, samtools does need it for cram
m
Matthias De Smet
10/02/2025, 10:13 AMI knew it! 😄
s
Sam Wilkinson
10/02/2025, 10:13 AMI have no idea WHY it's needed, surely all the necessary info is there
Sam Wilkinson
10/02/2025, 10:13 AMbut whatever, far be it from me to question heng
m
Matthias De Smet
10/02/2025, 10:14 AMOtherwise I would’ve made it optional.
Past me wasn’t an idiot 🎉
s
Sam Wilkinson
10/02/2025, 10:14 AMI still think it should be a ternary though
Sam Wilkinson
10/02/2025, 10:14 AMso that BAM users don't have to provide it
m
Matthias De Smet
10/02/2025, 10:15 AMAh, yes, you are right.
Perhaps also include a check so it fails if the input is cram and no ref is provided
👍 1
s
Sam Wilkinson
10/02/2025, 10:47 AMm
Matthias De Smet
10/02/2025, 10:48 AMNice testing too!
👍 1
s
Sam Wilkinson
10/02/2025, 10:49 AMcheers, thanks for the fast review