Changes between Version 4 and Version 5 of DataManagement


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Timestamp:
Feb 9, 2011 8:06:36 AM (11 years ago)
Author:
laurent
Comment:

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  • DataManagement

    v4 v5  
    4747   * 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.
    4848   * Except where it references specific names using another convention (ex: sample name), file names should be all small letters.
    49  * Sample-level files should be named using: ''step_id.step_name.sample_name.genome_build.time_stamp.extension''
    50    * 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: ''vc02.unified_genotyper.A2a.human_g1k_v37.2011_02_01_12_00.snp''
    51  * Lane-level files should be named using: ''step_id.step_name.sample_name.lane_name.genome_build.time_stamp.extension''
    52    * 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''
     49 * Sample-level files should be named using: ''sample_name.step_id.step_name.genome_build.time_stamp.extension''
     50   * 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''
     51 * Lane-level files should be named using: ''sample_name.lane_name.step_id.step_name.genome_build.time_stamp.extension''
     52   * 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''
    5353 * Log file names should correspond to their output counterparts and have the .log extension.
    54    * 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''
    55    * 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''
    56 
     54   * 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''
     55   * 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''
    5756== Logging ==
    5857The 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.