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1. In several tutorials (MultiQC, fastp, Advanced Breseq) I gave example command line for loops that can be used to generate commands files for large numbers of samples. 
2. Often I use a python script to generate files like this, as I am more fluent in python coding than I am in bash/command line scripting.
3. Sometimes I generate some commands in Excel 
   1. An example might be a formula of '="breseq -j 6 -p -r Ref.gbk -o Run_output/" & A1 & " " & B1 & " " & C1 & " >& runLogs/" & A1' with sample name in A1, read1 in B1 and read2 in C1.
4. In a program like BBedit/notepad to copy paste the same command multiple times and change it as appropriate then paste the text directly into a nano editor on TACC.
5. In the introduction tutorial, several alternative text editor programs were mentioned with different ssh connectivity

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# remember that things after the # sign are ignored by bash
cat GVA2022.output.txt > end_of_class_job_submission.final.output
mkdir $WORK/GVA2022
mkdir $WORK/GVA2021/end_of_course_summary/  # each directory must be made in order to avoid getting a no such file or directory error
cp end_of_class_job_submission.final.output $WORK/GVA2022/end_of_course_summary/
cp what_i_did* $WORK/GVA2022/end_of_course_summary/  # note this grabs the 2 output files generated by tacc about your job run as well as the .slurm file you created to tell it how to run your commands file
 
cp commands $WORK/GVA2022/end_of_course_summary/

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