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Revision as of 14:51, 30 June 2015
, 14:51, 30 June 2015→Overall Pipeline Definition
* BATCH_TYPE
* BATCH_TYPE
* IGNORE_SM_CHECK - turn off the default validation that the @RG SM tag matches the bam list sample name.
* IGNORE_SM_CHECK - turn off the default validation that the @RG SM tag matches the bam list sample name.
* IGNORE_REF_CHR_CHECK
* IGNORE_REF_CHR_CHECK - turn off the default validation that checks that all of the BAM's chromosomes are in the reference file - eventually we may update to just validate those in CHRS.
* OUT_DIR
* OUT_DIR
* BAM_LIST
* BAM_LIST
* The BAM_LIST file can contain config values within it - the overall pipeline section will be checked for those config values.
* The BAM_LIST file can contain config values within it - the overall pipeline section will be checked for those config values.
* By default if a value is not defined in the section, it will check global.
* By default if a value is not defined in the section, it will check global.
==== Configure Each Step ====
==== Configure Each Step ====
