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Created with Raphaël 2.2.029Oct2827262523222120191615141312987652130Sep29282725242322211817161413111098765432131Aug30292827262524232221201918171615Fix fai checkFixed summary file nameAdded reference to bamMetricsMerge remote-tracking branch 'remotes/origin/develop' into fix-shiva_failsChanged error handelingVersion cleanup, point all to version 0.5.0Added bammetrics when start from bam fileHide QC from report when flexiprep is not executedchange pipeline test, not test on sambambaview, but on samtoolsviewMore style fixesMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gearsStyle changeRemove sambamba and use samtools for extracting pairs of unmapped reads (not the advanced query)Style fixes and config for samtofastqFixed link to bai fileFixed library keyNo memory increase on first retryAdded a merge stepFixed sample settingsAdded argsFixed md5 checkAdding Scaladocs to KrakenReportToJson and remove redundant codeStyle changeRefactor the report generation a bit. Move pipeline specific report components into the pipeline itself (not hosted in core anymore)Merge branch 'fix-coverage_piping' into 'develop' Fixes for the comments made in the ticket #241Fixed reportQuick fix, error in the HelloPipelineMerge remote-tracking branch 'remotes/origin/develop' into fix-shiva_failsMerge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gearsMerge branch 'feature-genotype_concordance' into 'develop' fixed missing keyRemoved double indexFix sample flagChanged file nameFix typeAdded input files to summary of shivaAdded more setting to the reportHide variant report when multisample variantcalling is not executedFix outputDir to workDir (makes more sense in multi sample mode)