Changes between Version 1 and Version 2 of DataManagement

Timestamp:

Feb 8, 2011 3:49:50 PM (15 years ago)

Author:

laurent

Comment:

--

DataManagement

@@ -50 +50 @@
  * Lane-level files should be named using: ''step_id.step_name.sample_name.lane_name.genome_build.time_stamp.extension''
    * Ex: A bam file for the lane FC20005_L1 of the sample A2a produced by the step pe03 (step 3 of paired-end alignment) with the tool BWA sampe using genome build human_g1k_v37 on a  run that begun on February 1st 2011 at 12:00 should be named: ''pe03.bwa_sampe.A2a.FC20005_L1.human_g1k_v37.2011_02_12_00.bam''
+ * Log file names should correspond to their output counterparts and have the .log extension. 
+   * Ex: log file for the vcf sample-level step above should be: ''vc02.unified_genotyper.A2a.human_g1k_v37.2011_02_01_12_00.log''
+   * Ex: log file for the bam lane-level step above should be: ''pe03.bwa_sampe.A2a.FC20005_L1.human_g1k_v37.2011_02_12_00.log''
+
+== Logging ==
+The logging strategy is currently under development but will be composed of both file logs and database entries in a Molgenis platform. The status is described below.
+
+=== Log Files ===
+ * At each step of the pipeline a single log is produced and contains:
+   * PBS out and err
+   * Tool out and err
+   * Other tool-produced log where applicable
+ * For log file naming, see section above.
+
+=== Molgenis ===
+The Molgenis