I have just started using org-mode and org-babel as a lab notebook. I am trying to use a code block to fill in two columns of a table. The code block seems to work for the first column because those are the right numbers. However, when trying to concatenate a string to the file name in column three so the code blocks works on a different set of files it seems to just run the code block on the original files instead, which produces the same output as column one.
#+name: tRNAs
#+begin_src sh :var filename="" :results silent
cd Data/tRNA
grep -c ">" $filename
#+end_src
#+tblname: sequences
| # of Sequences before QC | # after QC | Original File name|
|--------------------------+------------+------------------|
| 681865 | 681865 | read1 |
| 324223 | 324223 | read2 |
| 1014578 | 1014578 | read3 |
| 971965 | 971965 | read4 |
| 931777 | 931777 | read5 |
| 810798 | 810798 | read6 |
| 965134 | 965134 | read7 |
| 718474 | 718474 | read8 |
|--------------------------+------------+------------------|
#+TBLFM: $1='(org-sbe tRNAs (filename (concat "\"" $3 "\"")))
#+TBLFM: $2='(org-sbe tRNAs (filename (concat "\"final_" $3 "\"")))
