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| * 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 |
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| * 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 |
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| * 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. |
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| ==== Configure Each Step ==== | | ==== Configure Each Step ==== |
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| * <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> |
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| * <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> |
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| == Example Pipelines Created == | | == Example Pipelines Created == |
| Look for sections & <code>STEPS</code> in the defaults. | | 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/master/bin/gotcloudDefaults.conf |
| + | https://github.com/statgen/gotcloud/blob/alignPrep/bin/gotcloudDefaults.conf |