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Revision as of 14:55, 31 August 2015
, 14:55, 31 August 2015→Command Line Parameters: fix formatting about BAM_LIST
* NO_CRAM - do not allow CRAM files as input
* NO_CRAM - do not allow CRAM files as input
* MAKE_BASE_NAME_PIPE - base makefile name
* MAKE_BASE_NAME_PIPE - base makefile name
* MAKE_OPTS - otpions to pass to the make command that runs the jobs.
* MAKE_OPTS - options to pass to the make command that runs the jobs.
* BAM_DEPEND - set to TRUE if you want the BAM file to be included as a make dependency
* BAM_DEPEND - set to TRUE if you want the BAM file to be included as a make dependency
* <code>--maxlocaljobs</code> <number> - number of jobs to allow to run when batchtype is local (default 10) - does not validate for commands running LOCAL
* <code>--maxlocaljobs</code> <number> - number of jobs to allow to run when batchtype is local (default 10) - does not validate for commands running LOCAL
* <code>--region</code> <region to process> - like snpcall, specifies a single region to process
* <code>--region</code> <region to process> - like snpcall, specifies a single region to process
* <code>--bam_list|list|bamlist|bam_index|bamindex</code> <bam list file> - overrides
* <code>--bam_list|list|bamlist|bam_index|bamindex</code> <bam list file> - overrides <code>BAM_LIST</code>, the list of sample bam files to process
<code>BAM_LIST</code> list of sample\tbam to process
* <code>--out_dir|outdir</code> <output directory> - overrides <code>OUT_DIR</code>
* <code>--out_dir|outdir</code> <output directory> - overrides <code>OUT_DIR</code>
* <code>--batchtype</code> <type> - overrides <code>BATCHTYPE</code>
* <code>--batchtype</code> <type> - overrides <code>BATCHTYPE</code>
* <code>--keeptmp</code> - overrides <code>KEEP_TMP</code>
* <code>--keeptmp</code> - overrides <code>KEEP_TMP</code>
* <code>--keeplog</code> - overrides <code>KEEP_LOG</code>
* <code>--keeplog</code> - overrides <code>KEEP_LOG</code>
== Example Pipelines Created ==
== Example Pipelines Created ==
