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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
# [[#Overall Pipeline Definition|Overall Pipeline Definition]]
# [[#Overall Pipeline Definition|Overall Pipeline Definition]]
#* Basics for the overall pipeline
#* Basics for the overall pipeline
#* '''NOTE: Curretnly, configurations set in the overall pipeline's section do not by default pass onto the step's configurations'''
#* '''NOTE: Currently, configurations set in the overall pipeline's section do not by default pass onto the step's configurations'''
# [[#Configure Each Step|Configure Each Step]]
# [[#Configure Each Step|Configure Each Step]]
* 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
* UNIFORM_TARGET_BED
* UNIFORM_TARGET_BED
* OFFSET_OFF_TARET
* OFFSET_OFF_TARET
* CHRS
* CHRS - defines which chromosomes to run.
* UNIT_CHUNK
* UNIT_CHUNK
* 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
* 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 ====
** be its own Makefile target/.OK file
** be its own Makefile target/.OK file
** run independently on the cluster
** run independently on the cluster
== Command Line Parameters ==
Required Parameters:
* <code>--name</code> <pipelineName> - name of the pipeline to run
* <code>--conf</code> <configuration file> - configuration file to use
NOTE: Currently, any "overrides" are for the global setting only - not for the pipeline/step.
* this needs to be fixed so they can override the pipeline settings
Optional Parameters:
* <code>--ignoreSmCheck</code> - overrides <code>IGNORE_SM_CHECK</code>
* <code>--ignoreRefChrCheck</code> - overrides <code>IGNORE_REF_CHR_CHECK</code>
* <code>--verbose</code> <number> - verbose value passed to the loadConf method
Optional Parameters like SnpCall:
* <code>--numjobs|numjobs</code> <number> - number of jobs to run in parallel
* <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>--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>--out_dir|outdir</code> <output directory> - overrides <code>OUT_DIR</code>
* <code>--batchtype</code> <type> - overrides <code>BATCHTYPE</code>
* <code>--batchopts</code> <options> - overrides <code>BATCHOPTS</code>
* <code>--chrs|chroms</code> <comma separated chromosomes> - overrides <code>CHRS</code> (CHRS is space separated - commas are converted to spaces)
* <code>--ref_dir|refdir</code> <reference directory> - overrides <code>REF_DIR</code>
* <code>--ref_prefix|refprefix</code> <prefix> - overrides <code>REF_PREFIX</code>
* <code>--bam_prefix|bamprefix</code> <prefix> - overrides <code>BAM_PREFIX</code>
* <code>--base_prefix|baseprefix</code> <prefix> - overrides <code>BASE_PREFIX</code>
* <code>--gotcloudroot|gcroot</code> <path to gotcloud> - by default gotcloud root is determined from the path to the pipeline script, but this setting overrides that.
* <code>--help</code> - print Usage
* <code>--test</code> <test directory> - run the test code (just for indel right now)
Unused command line options:
* In the code, but are not actually used:
* <code>--keeptmp</code> - overrides <code>KEEP_TMP</code>
* <code>--keeplog</code> - overrides <code>KEEP_LOG</code>
== Example Pipelines Created ==
Look for sections & <code>STEPS</code> in the defaults.
https://github.com/statgen/gotcloud/blob/master/bin/gotcloudDefaults.conf
https://github.com/statgen/gotcloud/blob/alignPrep/bin/gotcloudDefaults.conf
