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 |