| | 1 | === Pipeline Result Files Naming Convention === |
| | 2 | The 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 == |
| | 15 | 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. |
| | 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 === |
| | 25 | 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: |
| | 26 | |
| | 27 | * Molgenis instance created with proposed model |
| | 28 | * Scripts for insertion under development |
