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Revision as of 15:05, 20 November 2012
, 15:05, 20 November 2012→Running the Mapping Pipeline
* index_file INDEX_FILE_NAME - name of the index file
* index_file INDEX_FILE_NAME - name of the index file
** May also be specified via INDEX_FILE in the configuration file
** May also be specified via INDEX_FILE in the configuration file
** Required to be set either via command-line or configuration* ref_dir REFERENCE_DIR - value to set config key REF_DIR to, overriding other values, REF_DIR can then be used inside config files.
** Required to be set either via command-line or configuration
* ref_dir REFERENCE_DIR - value to set config key REF_DIR to, overriding other values, REF_DIR can then be used inside config files.
** May also be specified via REF_DIR in the configuration file
** May also be specified via REF_DIR in the configuration file
* fastq FASTQ_PATH - prefix path to the fastq files specified in the INDEX_FILE
* fastq FASTQ_PATH - prefix path to the fastq files specified in the INDEX_FILE
