Closed Leonievb closed 2 years ago
Regarding compressed barcodes.tsv.gz
: We need to add a test for this. What exactly gives an error?
We support two CellRanger directory layouts, see https://github.com/frisen-lab/TREX/blob/main/src/trex/cellranger.py.
The CellRanger 2 layout:
outs/filtered_gene_bc_matrices/
barcodes.tsv
The CellRanger 3 layout:
outs/filtered_feature_bc_matrix/
barcodes.tsv.gz
We detect the format automatically depending on whether a filtered_gene_bc_matrices
or filtered_feature_bc_matrix
subfolder exists in the outs/
folder.
You wrote filtered_feature_bc_matrices
("feature" and plural "matrices"), which is a combination of the two. Is that a typo or is the directory really named that way?
To your first question: I haven't seen that error myself but I got told by someone using the code that this happened only when trying to run the pipeline on the test data with the -f flag. If required, I can request the person to reproduce the error and send the error message.
To the second question: This was a typo from my side, I am sorry for confusion! The layouts of CelllRanger 2 and 3 are exactly as you write it. And the person I talked to said she had to rename folders to the CellRanger 3 layout as soon as she used extra arguments. I will ask her to send more details. This is of interest for issue #10 and will be posted there
The person reporting issues on folder name and compression of files could not reproduce the error. Therefore I would keep the folder names and files as they are and also close this issue for now
The folder structure of this git repository is inconsistent and confusing. For example,
expected
can be moved to/tests/expected
chrTomato-N.fa
in/tests/data/outs/
should be moved to/tests/data/
/tests/data/outs/filtered_gene_bc_matrices
should be renamed to/tests/data/outs/filtered_feature_bc_matrices
barcodes.tsv
,genes.tsv
andmatrix.mtx
in/tests/data/outs/filtered_gene_bc_matrices)/hg38_Tomato-N/
are expected to be compressed (e.g.barcodes.tsv.gz
by the algorithm and algorithm gives error if not