Allow bam files to be added as input to rnavar workflow

[jaybee84]

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]

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

Thanks.

[FerranLlobetC]

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

Thanks!

[expansion-bioemformatics]

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]

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

[maxulysse]

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.

[amnahsiddiqa]

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.

@maxulysse Do we have any update on this? Thanks

[nvnieuwk]

BAM/CRAM file support has been added into the dev branch