Usage: microcat config [OPTIONS]
Quickly adjust microcat's default configurations
Options:
--star_ref PATH STAR reference genome for aligning bulk
sequencing data
--starsolo_ref PATH STARsolo reference genome for aligning
single and spatial sequencing data
--cellranger_ref PATH Cellranger reference genome for aligning
single sequencing data
--krak2_ref PATH Kraken2 reference genome for aligning
microbiome data
--krakuniq_ref PATH Samples list, tsv format required.
--pathseq_ref PATH Samples list, tsv format required.
--download_dir PATH Download path for aligning microbiome data
--metaphlan4_ref PATH Samples list, tsv format required.
--generic_profile [lsf|slurm|pbs]
Samples list, tsv format required.
-e, --edit [single|bulk|spatial|multi]
Edit config file
-h, --help Show this message and exit.
