A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello. Is there some interest for a nf-core module that sorts a bed/vcf file before compressing it with tabix ? All in one module with a pipe

Does `sort` not already provide/expose the `-O` and `-W` options which allow setting compression and indexing of the VCF as part of command? 

Right, I see. Yes for VCF files, I can use `bcftools sort` to sort + compress + index in one command. That’s the best. Thank you :bow: !

Do you know a similar trick for BED files :sweat_smile: ?

(sorry, there’s a mistake in my OP. I meant compressing _with bgzip_. Essentially trying to recreate the first command of this example from the tabix manpage
```(grep "^#" in.gff; grep -v "^#" in.gff | sort -t"`printf '\t'`" -k1,1 -k4,4n) | bgzip &gt; sorted.gff.gz;
tabix -p gff sorted.gff.gz;
tabix sorted.gff.gz chr1:10,000,000-20,000,000;```


Hmm. Well BCFtools is bgzip compression internally. So for VCF still use `bcftools/sort`. For this second issue though I am not aware of any existing module 