error in rule bigwig about armor

[csoneson]

Not at a stable connection right now, but we do have sort -k1,1 -k2,2n in the bigwig rule, so it may be a problem with the LC_COLLATE=C part. Could you try to see whether adding LC_COLLATE=C just before sort here helps:

ARMOR/Snakefile

Line 471 in 3bfc403

"bedtools genomecov -split -ibam {input.bam} -bg | sort -k1,1 -k2,2n > "

[rrdavis77]

I'll add it and let you know if that solves it.
Thanks

[rrdavis77]

I changed the snake file line 471 by adding LC_COLLATE=C and it solved the issue.

"bedtools genomecov -split -ibam {input.bam} -bg | LC_COLLATE=C sort -k1,1 -k2,2n > "

[csoneson]

Great, thanks. We’ll fix that.