CODEWITHSUNDEEP
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sureshhewabi
sureshhewabi

Reputation: 91

append a parameter to a command in the file and run the appended command

I have a the following command in a file called $stat_val_result_command. I want to add -Xms1g parameter at the end of the file so that is should look like this:

  <my command in the file> -Xms1g

However, I want to run this command after append. I am running this in a workflow system called "nextflow". I tied many things, including following, but it does not working. check the script section which runs in Bash by default:

    process statisticalValidation {

   input:
   file stat_val_result_command from validation_results_command.flatten()

   output:
   file "*_${params.ticket}_statistical_validation.txt" into validation_results

   script:
   """
   echo " -Xms1g"  >> $stat_val_result_command && ```cat  $stat_val_result_command```
   """
}

Upvotes: 1

Views: 536

Answers (1)

Steve
Steve

Reputation: 54502

Best to avoid appending to or manipulating input files localized in the workdir as these can be, and are by default, symbolic links to the original files.

In your case, consider instead exporting the JAVA_TOOL_OPTIONS environment variable. This might or might not work for you, but might give you some ideas if you have control over how the scripts are being generated:

export JAVA_TOOL_OPTIONS="-Xms1g"
bash "${stat_val_result_command}"

Also, it's generally better to avoid localizing and running scripts like this. It might be unavoidable, but usually there are better options. For example, third-party scripts, like your Bash script could be handled more simply:

Grant the execute permission to these files and copy them into a folder named bin/ in the root directory of your project repository. Nextflow will automatically add this folder to the PATH environment variable, and the scripts will automatically be accessible in your pipeline without the need to specify an absolute path to invoke them.

This of course assumes you can control and parameterize the process that creates your Bash scripts.

Upvotes: 1

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