this part uses the index to read the gtf file but it seems uncertain if that file is compressed or not. 10x indexes for cell ranger are not but arc are. cell ranger (7) mkref are too.
may be dependent on cell ranger versions?
nextflow should check which exists so the right file is staged
this part uses the index to read the gtf file but it seems uncertain if that file is compressed or not. 10x indexes for cell ranger are not but arc are. cell ranger (7) mkref are too.
may be dependent on cell ranger versions?
nextflow should check which exists so the right file is staged
https://github.com/ChristopherBarrington/scamp/blob/f1a742012360f4d9829c122c6431f030c61cc3c4/workflows/seurat/prepare/cell_ranger/main.nf#L52
linked to #83