diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index de8bf9658ae2ba16f28f65f753f7a8bdb26949e8..8b6166a818a89b87f9c942eef11d6a68204ad78d 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -13,6 +13,7 @@ params.deriva = "${baseDir}/../test_data/auth/credential.json" params.bdbag = "${baseDir}/../test_data/auth/cookies.txt" //params.repRID = "16-1ZX4" params.repRID = "Q-Y5JA" +params.source = "dev" params.refMoVersion = "38.p6.vM22" params.refHuVersion = "38.p12.v31" params.refERCCVersion = "92" @@ -34,6 +35,13 @@ logsDir = "${outDir}/Logs" // Define fixed files derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json") +if (params.source == "dev") { + source = "dev.gudmap.org" +} else if (params.source == "staging") { + source = "staging.gudmap.org" +} else if (params.source == "production") { + source = "www.gudmap.org" +} //referenceBase = "s3://bicf-references" referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references" referenceInfer = Channel.fromList(["ERCC","GRCh","GRCm"]) @@ -100,7 +108,7 @@ process getBag { # deriva-download replicate RID echo -e "LOG: fetching bagit for ${repRID} in GUDMAP" >> ${repRID}.getBag.log - deriva-download-cli staging.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID} + deriva-download-cli ${source} --catalog 2 ${derivaConfig} . rid=${repRID} echo -e "LOG: fetched" >> ${repRID}.getBag.log """ }