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, 13:08, 30 June 2015→Defining a New Pipeline
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=== 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
<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:
