suggestions for exceptions and tutorial updates #11
Description
For README of chromap, directions for putting "bam" or "fragments" after "run_chromap align" are missing.
For installation, the link for docker container is pointing at dev version which is missing "-o" parameter for run_chromap align bam runs. This seems to be already fixed for run_chromap.py script on github as well as version 1.1 of docker container.
For README of kallisto, it would be also helpful to put "no compression" sign for barcode_onlist similar to chromap README since it won't read compressed barcode whitelist. Might be better to put exceptions or error messages within the script since it's easy to miss when using barcode whitelists within cellranger files or downloaded ones from IGVF portal.
Also, there is an issue with the last steps of the run (tar the directory) if input string for "output_dir" contains trailing slash at the end. With the trailing slash, the tar file is being saved within the output_dir as ".tar.gz" while trying to compress the output_dir which causes errors.
Also the tutorial seems to suggest .h5ad output being located in the counts_unfiltered directory when in fact it is in the parent directory of output_dir.