[BUG] File converted crashes on non-unique gene index

[KrisDavie]

Describe the bug
Any sample put through the file converter with duplicate genes will cause the pipeline to crash because of this line: https://github.com/vib-singlecell-nf/vsn-pipelines/blob/master/src/utils/bin/sc_file_converter.py#L139

The sort fails because of the duplicate elements.
Adding adata.var_names_make_unique() before this line (https://anndata.readthedocs.io/en/stable/anndata.AnnData.var_names_make_unique.html) adds a suffix to the gene names and allows the sort.

To Reproduce
Steps to reproduce the behavior:

1. Configure with these options:

nextflow config vib-singlecell-nf/vsn-pipelines -profile singularity,tenx,single_sample > nextflow.config

2. Run using this entry point:

nextflow -C nextflow.config run vib-singlecell-nf/vsn-pipelines -entry single_sample

Must be done on a sample with duplicate gene names

3. See error:

Lost the error in scroll history, but it was during the converter step and the error was that it could not be reindexed with duplicate values

Expected behavior
Continuation with no error

Please complete the following information:

• OS: Ubuntu 18.04
• Nextflow Version: 19.12.0-edge
• vsn-pipelines Version: e.g. 0.15.1

[dweemx]

This is fixed in 7c400ea