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| * 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 |
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| ** 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> 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. |
| + | https://github.com/statgen/gotcloud/blob/master/bin/gotcloudDefaults.conf |