=== Pipeline Result Files Naming Convention ===
The following convention applies to all files that are generated by the pipeline. For containing folders, see sections above.

 * General convention
   * Filenames are composed of tokens identifying their content. The tokens are separated by '.' and if necessary the words within the tokens can be separated by '_' for reading purpose.
   * Except where it references specific names using another convention (ex: sample name), file names should be all small letters.
 * Sample-level files should be named using: ''sample_name.step_id.step_name.genome_build.time_stamp.extension''
   * Ex: A vcf file for the sample A2a produced by the step vc02 (step 2 of variant calling) with the tool !UnifiedGenotyper using genome build human_g1k_v37 on a run that begun on February 1st 2011 at 12:00 should be named: ''A2a.vc02.unified_genotyper.human_g1k_v37.2011_02_01_12_00.snp''
 * Lane-level files should be named using: ''sample_name.lane_name.step_id.step_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: ''A2a.FC20005_L1.pe03.bwa_sampe.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: ''A2a.vc02.unified_genotyper.human_g1k_v37.2011_02_01_12_00.log''
   * Ex: log file for the bam lane-level step above should be: ''A2a.FC20005_L1.pe03.bwa_sampe.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 platform will be used to provide a more advanced and general view of the status of the pipeline runs (including different views, sorting, etc.) The current status is:

 * Molgenis instance created with proposed model
 * Scripts for insertion under development