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Created with Raphaël 2.2.023Feb19181615131211109874129Jan282726252019181514121110987654330Dec292827171475230Nov20191413121110931Oct20Sep14131211109Use datahub as source for integration_se ciFix ci lintReplace species inference with seqwhoMerge branch 'dnanexus' into 'develop'Change nextflow run locations for CI to rootMerge branch 'develop' into 'dnanexus'Update file refs in .nf to match new locationsUpdate CHANGELOGAdd dnanexusExample.json fileUpdate README.mdAdd to cleanupMove non nextflow configs back to workflow and symlink filesAdd test for seq type failureUtilize seq type inference from seqwhoFix missing auth file processesFix align machinetype in d dnanexus configAdd cpu/mem to dnanexus configFix bigwig output name patternLink deriva credentials for upload processed files and fix logsLink deriva credentials for upload input/output bagsMove fastq count before cpChange bdbag to use cookie locallyChange symlink to cp for cookie in getDataTry removing stage-as from getDataAdd quotes around find predicateConvert ls to findFix input folders to match nf being in baseFix zip nameUse predicted name of inputBag zip instead of using lsAdd configs and nf to root for nextflow standardMove config/nf for nextflow standardRemove docker prefixChange containers for dnanexus to have prefix docker://Change dnanexus executorAdd dummy main.nfFix nf filenameNextflow-ifyNextflow-ifyAdd local configsFix datahub ref download