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Revision as of 02:13, 7 November 2012
, 02:13, 7 November 2012no edit summary
See [[#Sequence Index File|Sequence Index File]] for how to set the index file either via command line options or via configuration.
See [[#Sequence Index File|Sequence Index File]] for how to set the index file either via command line options or via configuration.
==== Turning Off Optional Steps====
==== Turning Off Optional Steps====
* out_dir OUTPUT_DIR - directory for the output
* out_dir OUTPUT_DIR - directory for the output
** May also be specified via OUT_DIR in the configuration file
** May also be specified via OUT_DIR in the configuration file
** Required to be set either via command-line or configuration
* conf CONFIG_FILE - configuration file
* conf CONFIG_FILE - configuration file
* 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
* 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
