General
* Added the optional arguments `--kallisto` and `--bustools`, which may be used to override the packaged kallisto and bustools binaries. The argument may be a command in the user's PATH, which will be expanded to the full absolute path, or an absolute/relative path to the binary (109, thanks apeltzer, dpryan79, Maarten-vd-Sande).
`ref`
* Any spaces in GTF groups are now removed. For instance, if a transcript has ID `TRANSCRIPT ID` then the resulting transcript sequence will be named `TRANSCRIPTID`. (97, thanks axelalmet)
`count`
* Fixed an issue where converting the count matrix using `--loom` and `--workflow lamanno` would cause an error (91)
* Fixed an issue with parsing FASTQ paths when using `-x smartseq`, where the second read file would be erroneously used as the first (114, thanks jma1991)
* Added entries to indicate the current working directory when the `kb` command was called, along with the `kallisto` and `bustools` binary paths and versions in `kb_info.json`.