search

nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
31 stars 31 forks source link

Allow bam files to be added as input to rnavar workflow #41

Open jaybee84 opened 2 years ago

jaybee84 commented 2 years ago

Description of feature

I have aligned files using the nfcore RNAseq pipeline (bam). I would like to use them to launch the rnavar pipeline to avoid re-doing the alignment. This will save time and resources for large scale data processing.

gurpreet-bioinfo commented 2 years ago

Are there any updates here? I am also interested to use markdup.sorted.bam output from nf-core/rnaseq pipeline.

Thanks.

FerranLlobetC commented 1 year ago

Hi 👋 I am in the exact same situation. Any updates regarding this issue?

Thanks!

expansion-bioemformatics commented 1 year ago

Also interested in using previously generated bams (in my case from the rnasplice pipeline). Any updates appreciated! Would love to not be repeating steps using precious AWS $$$

amnahsiddiqa commented 2 months ago

I also am looking for this feature and would appreciate any update?Thanks

maxulysse commented 2 months ago

Hi all, I'm currently working on updating the pipeline with the the latest template sync, once this is done, I will work on adding extra features towards a release. Current ETA is around 3 month for the release, but I know that this is a highly requested feature, so I'll try to prioritize towards it.