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Created with Raphaël 2.2.028Feb242319181615131211109874129Jan282726252019181514121110987654330Dec292827171475230Nov20191413121110931Oct20Sep1413121110Disconnect confidence from species and seq type inferenceAdd quotes to seqwho errorAdd quotes to seqwho errorMerge dnanexus changesFix nf reference in ciMove nf and confs to match nextflow formatAdd back mkdir -p in seqwho unit testTry removing ./ from seqwho -f in unit testMake dummy dir for plotsFix seqwho version collection in ciUse 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 standard