2a) make a directory in your project called scripts and (b) upload your new script there.
3) In the dx command proper, execute the script. [ -icmd="sh script.sh" ]
4) make sure the location of that script is one of your -iin= files [ -iin="path/to/your/script.sh"] of the dx command and whatever files the script will be working on are also listed as -iin files
I personally would use the regenie workflow scripts from the gwas github page as a guideline:
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It is not only possible, it is quite easy.
1) Write your script.
2a) make a directory in your project called scripts and (b) upload your new script there.
3) In the dx command proper, execute the script. [ -icmd="sh script.sh" ]
4) make sure the location of that script is one of your -iin= files [ -iin="path/to/your/script.sh"] of the dx command and whatever files the script will be working on are also listed as -iin files
I personally would use the regenie workflow scripts from the gwas github page as a guideline:
https://github.com/dnanexus/UKB_RAP/tree/main/GWAS/regenie_workflow
You can also use the semicolon ";" as a command delimiter just as you would in linux.
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