Slack admin can choose which channel should be disabled from notification.
To disable a channel from notification:
Step 1: Log in to JIRA Server as an administrator
Step 2: Choose Settings button at top right corner 
Step 3: At drop down menu, select System
Step 4: At the right hand side, scroll down until Slack Integration option > choose App setting
Step 5: Choose Access control tab
Step 6: Enter channels list in to text field that you don't want to setup notification in project setting (start with # for public channel, ? for private channel). Then click on Save button
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