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, 13:08, 30 June 2015
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| </ul> | | </ul> |
| === Defining a New Pipeline === | | === Defining a New Pipeline === |
| + | |
| + | There are 2 parts for creating a new pipeline |
| + | # [[#Overall Pipeline Definition|Overall Pipeline Definition]] |
| + | #* 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''' |
| + | # [[#Configure Each Step|Configure Each Step]] |
| + | |
| + | ==== Overall Pipeline Definition ==== |
| <ol> | | <ol> |
| <li> Define a new configuration section for your pipeline | | <li> Define a new configuration section for your pipeline |
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| <ul><li> Note: each step must have its own configuration section</li></ul> | | <ul><li> Note: each step must have its own configuration section</li></ul> |
| </li> | | </li> |
| + | </ol> |
| + | |
| + | Optional Overall Pipeline Settings: |
| + | * BATCH_OPTS |
| + | * BATCH_TYPE |
| + | * IGNORE_SM_CHECK - turn off the default validation that the @RG SM tag matches the bam list sample name. |
| + | * IGNORE_REF_CHR_CHECK |
| + | * OUT_DIR |
| + | * BAM_LIST |
| + | * REF |
| + | * REF_FAI |
| + | * MULTIPLE_TARGET_MAP |
| + | * UNIFORM_TARGET_BED |
| + | * OFFSET_OFF_TARET |
| + | * CHRS |
| + | * UNIT_CHUNK |
| + | * NO_CRAM - do not allow CRAM files as input |
| + | * MAKE_BASE_NAME_PIPE - base makefile name |
| + | * MAKE_OPTS - otpions 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 |
| + | |
| + | |
| + | |
| + | NOTES: |
| + | * 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. |
| + | |
| + | |
| + | |
| + | ==== Configure Each Step ==== |
| + | <ol> |
| <li>Create a section for each step | | <li>Create a section for each step |
| <ul><li> Example: | | <ul><li> Example: |