ASAP Changelist V1.1.7

The following items have been changed/corrected or added in version 1.17 of ASAP.
Item Notes Date Completed
Added ability to run N serial jobs simultaneously Previously, serial jobs were literally each run in serial. Users can now specify how many processors to be used to make full use of the machine. Jan, 15, 2012
RealignBatch now allows smaller groupings Users can now specify smaller groupings within the RealignBatch step to ensure reasonable sharing is used, but much faster completion times Jan 10, 2012
Improved exome baselines The settings in the exome baseline is now better suited for much faster translation for medium to large datasets Jan 11, 2012
Bug fixes Some bugs associated with rerunning asap after a small number of jobs failed Jan 9, 2012

ASAP Changelist V1.1.6

The following items have been changed/corrected or added in version 1.1.6 of ASAP.
Item Notes Date Completed
Serial job reruns realignment Introduced by v 1.1.5, the recalibration step was deleting the realigned file in some cases which caused ASAP to attempt to reproduce them when ASAP was rerun. Dec, 19, 2012

ASAP Changelist V1.1.5

The following items have been changed/corrected or added in version 1.1.5 of ASAP.
Item Notes Date Completed
Error in Serial mode/recalibration Samtools was halting if the user specified KEEP_TEMPORARY_FILES to be TRUE during recalibration. This has been fixed Dec. 12, 2012

ASAP Changelist V1.1.4

The following items have been changed/corrected or added in version 1.1.4 of ASAP.
Item Notes Date Completed
Available tools listed in banner Previously, users had to consult the manual for the spelling of tools names. These are now listed for each run Dec. 4, 2012
Available templates listing Users can now issue the command LIST_TEMPLATES to see a list of each step and it's available templates. This is a live search, so even user generated templates will be listed Dec. 4, 2012
List templates for active steps Available templates for each active step is now listed in the banner of each run Dec. 4, 2012
Added ability to specifically calibrate the alignment step's runtime Alignment runtimes can very depending on the data. Users can adjust the alignment specific time calibration to avoid having their jobs killed by the scheduler for running over the requested time Dec. 5, 2012
Bug fix re: no input data Fixed an error associated with generating scripts to call SNPs even if there are no bams to use. ASAP now warns the user that no scripts were generated. Dec. 5, 2012
Bam import error with chromosome in directory structure Fixed an error preventing the regular expression describing a bam file's chromosome or sample ID to be found in the directory structure rather than in the file name itself. Dec. 5, 2012

ASAP Changelist V1.1.3

The following items have been changed/corrected or added in version 1.1.3 of ASAP.
Item Notes Date Completed
Added QPLOT as an optional step for basic bam statistics This is a new step nov, 2012
Created templates for each step Moved the erb into individual templates and enabled the user to be able to select from available templates to allow easier customization and flexibility Nov, 2012
Added support for GATK 2.0 GATK changed some flags and even one of the module names, requiring a small number of changes to the default settings and to the template Nov, 2012
Added support for flat files when setting up new projects When running IMPORT_BAM and GENERATE_BATCH, users can now provide a flat file instead of a regular expression Nov, 2012

ASAP Changelist V1.1.2

The following items have been changed/corrected or added in version 1.1.2 of ASAP.
Item Notes Date Completed
Alignment caused failures under certain circumentances Fixed an error where some conditions would cause ASAP to instruct samtools to index .bai files, which caused an error. Jun 27, 2012
Corrected status reporting Fixed a database query error preventing ASAP from correctly getting job lists based on status in certain situations. This affected several job related tools, such as STATUS, RECONCILE and SHOW_LOG Jun 27, 2012

ASAP Changelist V1.1.1

The following items have been changed/corrected or added in version 1.0.1 of ASAP.
Item Notes Date Completed
Basic summary for BAMs Added flagstat summary for bam files Jun 25, 2012
Bug fixes for PREP_SYSTEM Some issues with certain cases involving GATK and Picard getting linked improperly Jun 20, 2012
Issue with chgrp fixed ACCRE changed some security which caused chgrp to fail when performed within a cluster based job. Switched to using group sticky bit for all executors. Jun 20, 2012

ASAP Changelist V1.1.0

The following items have been changed/corrected or added in version 1.0.1 of ASAP.
Item Notes Date Completed
PREP_SYSTEM added Provide a method to allow the user to install tools using ASAP to simplify getting started Jun 12, 2012
Added halt feature when tools were outdated Previously, versions were simply reported. Now, ASAP will halt if the versions are older than expected. Jun 12, 2012

ASAP Changelist V1.1.0

The following items have been changed/corrected or added in version 1.0.1 of ASAP.
Item Notes Date Completed
infer Final/Intermed Dirs When generating sample configurations, ASAP now infers the location based on the CWD. This can be overridden by the user once they edit the configuration, but follows the standard approach we've been using internally. May 10, 2012
additional flags added Added flags for setting PICARD_PATH to allow users to set these paths during sample generation May 10, 2012
GENERATE_BATCH is slightly more tolerant of naming Added support for lower case "r" in paired end designation, and also expressly fails if the translation from 1 to 2 results in no change to the filename May 10, 2012
Removed Vanderbilt specific paths from a default setting The reference sequence had the default path to our local reference. That has been removed and defaults to an empty string May 10, 2012
Added some cmd line options Added command line options to simplify the generation of new configuration files. These include: PICARD_PATH. May 11, 2012
Accept relative paths for Reference Allow the user to specify reference sequence using relative path May 11, 2012
Relative defaults for FINAL and INTERMEDIATE If these don't exist as part of configuration or cmd-line, the program uses the current working directory to "bake" valid settings within the current directory. May 11, 2012
Added IMPORT_BAM functionality Users can import bam files as either aligned, realigned or recalibrated and they will fit into the pipeline as if they were processed by the application itself May 18, 2012
Added INDEL Users can call Indels using GATK (samtools to come very soon) May 22, 2012
Added support for annotations via Annovar Users can now utilize most annovar functionality after VCFs have been produced (indel and SNP) May 22, 2012
Improved Serial Execution Added halt on error to serial execution along with automatic start after scripts are generated (-j like cluster based autosubmit) May 22, 2012
Minor changes to database to allow concurrent steps to be run simultaneously This was necessary for INDEL/SNP parallel execution. As a result, most step's ranks were updated to be consistent for each primary step May 22, 2012
Executor Verification Check for group settings in configuration May 23, 2012
Options for MarkDupes and Fixmate Allow users to turn these off individually through configuration parameters May 23, 2012
Improved logging for Serial Executor Log capturing to same directories as used by cluster and halt on error May 23, 2012
Added Tools Type Tools are things that run within ASAP, such as ImportBam, GenerateBatch, etc. These no longer require RUN to execute May 24, 2012

-- EricTorstenson - 10 May 2012
Topic revision: r11 - 17 Jan 2013, EricTorstenson
 

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