Changes between Initial Version and Version 1 of DataManagement/FileNameConventions


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Timestamp:
Jul 15, 2011 8:50:46 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • DataManagement/FileNameConventions

    v1 v1  
     1=== Pipeline Result Files Naming Convention ===
     2The following convention applies to all files that are generated by the pipeline. For containing folders, see sections above.
     3
     4 * General convention
     5   * 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.
     6   * Except where it references specific names using another convention (ex: sample name), file names should be all small letters.
     7 * Sample-level files should be named using: ''sample_name.step_id.step_name.genome_build.time_stamp.extension''
     8   * 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''
     9 * Lane-level files should be named using: ''sample_name.lane_name.step_id.step_name.genome_build.time_stamp.extension''
     10   * 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''
     11 * Log file names should correspond to their output counterparts and have the .log extension.
     12   * 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''
     13   * 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''
     14== Logging ==
     15The 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.
     16
     17=== Log Files ===
     18 * At each step of the pipeline a single log is produced and contains:
     19   * PBS out and err
     20   * Tool out and err
     21   * Other tool-produced log where applicable
     22 * For log file naming, see section above.
     23
     24=== Molgenis ===
     25The 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:
     26
     27 * Molgenis instance created with proposed model
     28 * Scripts for insertion under development