irma-scripts
Stand-alone scripts deployed to Irma
These scripts are deployed to /proj/ngi2016001/private/scripts by the irma-provision process.
The scripts should contain instructions for usage unless it's obvious how to use them. Preferably, invoking a script without arguments should be safe to run without any side effects and only display usage instructions on stdout
NEVER put any passwords, usernames, tokens, user data or other sensitive information in the scripts. If such information is required by the script, rely on reading it from an environment variable instead.
When adding a new script to this repository, be sure to add a brief description of its purpose below:
- concordance_check.sh - bash script to perform concordance check between a vcf file with genotypes and a vcf file with variant calls
- find_unorganized_flowcells.sh - bash script that verifies that the organized project folder under the DATA directory contains all runfolders in incoming having data from the project in them
- link_project_sisyphus_reports.sh - bash script that links sisyphus runfolder reports from the incoming folder to the corresponding project folder under ANALYSIS
- set_charon_genotyping_status.sh - bash script to set the genotyping status field in charon to a specified value for samples present in a supplied vcf file
- statdump_to_json.pl - perl script that can parse a statdump zipfile created by sisyphus and output the statistics as json
- run_FastQC_and_MultiQC.sh - bash script to run FastQC on a specified project in a runfolder. The script will summarize the output in one or several MultiQC-reports.