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Syntax error in pre_analysis_first_script.sh #2

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MayankMurali opened this issue Feb 27, 2024 · 0 comments
Open

Syntax error in pre_analysis_first_script.sh #2

MayankMurali opened this issue Feb 27, 2024 · 0 comments

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@MayankMurali
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Hi - I am trying to integrate your wonderful pipeline. I came across the following error when running the pre_analysis_first_script.sh script:

pre_analysis_first_script.sh: line 48: syntax error near unexpected token `elif'
're_analysis_first_script.sh: line 48: `elif [[ $VCF_FILE_NAME =~ \bcf.gz$ ]]

I added the config file path to CONF_FILE in this script.
In the psrelip.config file, I have added the path to:

  • PLINK_HOME
  • PLINK2_HOME
  • TOOL_INSTALL_DIR
  • WD
  • VCF_FILE_NAME

Can you please help me solve this error. Thanks in advance!
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@MayankMurali