Outputs of CellRangerCount seem to contain duplicated files in an archive

[prioux]

CellRangerCount seems to create a folder with a bunch of files.

Inside that folder there is a .tgz archive that contain a duplication of the files already in that folder. That TAR file contains most, but not all of the files in the output folder.

This should be cleaned up. Either:

1. the tar file is completely redundant and should be removed before saving the output folder or
2. the tar file is supposed to be the final product (with a few less files) and we shouldn't even attempt to save the output folder.

How to check as a CBRAIN developer:

a) cd to the root of a finished CellRangerCount task
b) create the list of files in the output dir:

find cellranger_count_res -type f | sort >/tmp/listfiles  # adjust name of folder

c) create the list of files in the .tgz archive

tar -tzf cellranger_count_res/cellranger_count_res.mri.tgz | sort >/tmp/archfiles

d) Compare them with diff, or csdiff:

diff /tmp/listfiles /tmp/archfiles

[prioux]

Can we contact the CellRanger developers about that?

[natacha-beck]

We do not have direct contact with the dev team for this tool, it was integrated for users.

When look at the cellranger documentation, section Explore the output of cellranger count I feel like the only ouput that need to be saved is the outs folder.

I will confirm with the user.