Quantify RNA-seq reads with Salmon (metadata driven)
Input
FASTQ folder
Folder containing FASTQ(.gz) files; relative paths in metadata are resolved from here
Metadata (TSV)
Table with absolute-filepath (SE) or forward- & reverse-absolute-filepath (PE)
Salmon index
Transcriptome index created with `salmon index`
Output
Salmon quant folder
One sub-folder per sample with quant.sf, logs …
Configuration
threads
CPU threads
int4