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GotCloud: Creating a New Pipeline

2,508 bytes added, 14:50, 30 June 2015
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* CHRS- defines which chromosomes to run.
* NO_CRAM - do not allow CRAM files as input
** be its own Makefile target/.OK file
** 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> list of sample\tbam 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.

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