@sminot - Thanks for all your hard work Sam! I made one important change to preserve backwards compatibility with our lab. If there is a manifest.[csv, xslx] with [I1,I2,R1,R2] columns then use the "manifest" param in params.json like this. The "manifest" param will overload the "sample_information" and "fastq_list" params which our lab still uses.
@sminot - Thanks for all your hard work Sam! I made one important change to preserve backwards compatibility with our lab. If there is a manifest.[csv, xslx] with [I1,I2,R1,R2] columns then use the "manifest" param in params.json like this. The "manifest" param will overload the "sample_information" and "fastq_list" params which our lab still uses.