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Created with Raphaël 2.2.01Aug30Jul29282724232221181514327Jun26232119171312109654327May2621201514cutadapt config parse fixWrappers are now split in general and specific flexiprep extensionsChanged config back because of compatibility issuesRemove unused importsUpdate style and exclude JSON defs from style reformattingStyle reformattingFix bug in Flexiprep python summary scriptFix flexiprep summary json parsingFix on output directories of sha1sum and seqstatFix Ln import with new namespaceMerge remote-tracking branch 'upstream/peter'Flexiprep passes jobs to new summaryAdd gentrap scriptsAdd initial gentrap main interfaceUpdate base BiopetQScript command line argument namesFix Gentrap pom.xmlUse relative paths in empty cutadapt commandsUse relative symlinks by default in Flexiprep final filesAdd relative symlink option to Ln wrapperchanged function to extensionsInitial checkin for GentrapSeqstat now uses quality type dataFunction to get encoding of the fastq file, replaces python scriptSeqstat now uses quality type dataUpdate Seqtk wrapper namespaceUpdate scripts default location to follow Maven conventionUpdate flexiprep summary file nameOutput cutadapt statistics correctly in summary filesMerge commit 'cde8f1a6c35911120d75e8e3b3f4badb1c4c9562' into peterFix on fastqc jobsRevert "Fix on fastqc jobs"Fix on fastqc jobsSwitch to functionsFix on output variableExtend the .gitignore to ignore temp and swap files from vimMerge origin/master into peterMerge branch 'bow'Add cutadapt statistics output to flexiprep runsFirst version of summary of flexiprep in queue/scalaFunction to get encoding of the fastq file, replaces python script