v0.26.0

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.