search

MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
13 stars 5 forks source link

Idx folders not named properly #9

Open stu2 opened 6 years ago

stu2 commented 6 years ago

chkRefFiles is searching for folder ending in ".Idx" but the make-index function for hisat2 names it with a dash "genome-hisat2Idx". Also bwa doesn't appear to make any such folder. Thus I've only tested chkRefFiles with star and starWithAnn

serine commented 6 years ago

@stu2

This is still early days for this feature -refFiles. This an attempt to reuse previous generated index/reference files by previous RNAsik run.

I think you are referring to this block, right?

if(extn.startsWith(aligner)) {
    totRefFiles{"idx"} = refFile
}

Directory that holds index files is named by taking FASTA files name, dropping file extension i.e .fa/fasta and adding aligner specific suffix. And by the way aligner name passed through -align [star|hisat|bwa] e.g -align star -fastaRef check.fa then this will result in check.starIdx/ directory with relevant files. if align bwa -fastaRef check.fa then check.bwaIdx/

Back to that check block. if extension of check.bwaIdx, which is bwaIdx, starts with aligner then use those reference files. And you can check that all suffixes get set in sikIndexing.bds

Let me know if you meant something else

Thanks