A Docker container for the DKFZ Bias Filter.

This is a companion discussion topic for the original entry at https://dockstore.org/containers/quay.io/jwerner_dkfz/DKFZBiasFilter

[This comment is migrated over from disqus]

Custom adjustment for outputBinding is necessary:

  • output_vcf_file => “outputs”
  • output_qc_folder => “outputs”

below, the further variables in the JSON file are explained

  • write_qc => flag for writing qc results (true or false)
  • input_vcf => absolute path to your vcf file
  • input_bam => absolute path to your bam file
  • input_bam_index => absolute path to your bam index file
  • reference_sequence => absolute path to the reference sequence
  • reference_sequence_index => absolute path to the reference sequence index

run the dockstore client tool without the descriptor flag!

For testing, you can use the sample_config.json file in the git repository.

wget https://raw.githubusercontent.com/eilslabs/DKFZBiasFilter/master/sample_configs.json
dockstore tool launch --entry quay.io/repository/jwerner_dkfz/DKFZBiasFilter:1.2.1 --json sample_configs.json