Changes between Version 67 and Version 68 of BigCompute


Ignore:
Timestamp:
Mar 15, 2011 9:44:53 AM (7 years ago)
Author:
schaik
Comment:

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  • BigCompute

    v67 v68  
    77* UMCG: Morris Swertz, Freerk van Dijk
    88
    9 '''Description'''
     9=== Description ===
    1010Software is going to be implemented as workflow components. The workflows will run on the Dutch life science grid.
    1111
     
    1414* Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga (2010) Initial steps towards a production platform for DNA sequence analysis on the grid. BMC Bioinformatics 11: 1. Dec [http://www.ncbi.nlm.nih.gov/pubmed/21156038 pubmed]
    1515
    16 '''Implemented workflow components at AMC'''
     16=== Implemented workflow components at AMC ===
    1717
    1818This list of workflow components are already available. We can expand it with Pindel and (parts of) the GATK pipeline.
     
    2929* FastqC
    3030
    31 '''Implemented components of the Groningen pipeline'''
     31=== Implemented components of the Groningen pipeline ===
    3232
    3333Template (grid component)
    3434
    35 ''Alignment, realignment, recalibration, stats''
     35==== Alignment, realignment, recalibration, stats ====
    3636* pe0--fastqc.ftl (FastqToFastQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/quality/Workflow/FastqToFastQC.gwendia)
    3737* pe00-bwa-align-pair1.ftl (!BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
     
    5151* pe12-analyze-covariates.ftl (!GatkAnalyzeCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkAnalyzeCovariates.gwendia)
    5252
    53 ''Merge bam per sample and perform SNP and indel calling''
     53==== Merge bam per sample and perform SNP and indel calling ====
    5454* vc00a-unified-genotyper.ftl '''to do'''
    5555* vc00b-variant-filtration.ftl '''to do'''
     
    7474* Pindel (Pindel, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/pindel/Workflows/Pindel.gwendia)
    7575
    76 '''Data access rights'''
     76=== Data access rights ===
    7777
    7878To ensure that the most limited group of people has access to the data we have created a subgroup "gvnl" within the "vlemed" Virtual Organisation (VO).
     
    8383http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/DataManagement
    8484
    85 '''Things to address'''
     85=== Things to address ===
    8686* Available disk space on the grid storage elements / worker nodes
    8787