diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a27c94cc997964d4cd17377c39d032a75b60825..6e07862673964f559e751adb8ca119f9fd3ce238 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,7 @@ # v.2.0.1 (indev) **User Facing** * Corrected spelling of inferred (#125) +* Add param for seqwho reference (#127) **Background** * Corrected file search parameters due to name inconsistency (#129) @@ -11,6 +12,7 @@ * Remove "fail" integration CI tests (#133 addendum) * Add licence header to nf file, R and python scriptsand pytest scripts * Stop using RCB and RMB (default) with deriva.core insert calls to match server update (#134) +* Replace default seqwho reference location to one provided by source lab (#127) # v2.0.0 **User Facing** diff --git a/rna-seq.nf b/rna-seq.nf index 604fdaf1358ece0c51ab6f3f7313a180ead74638..f7875eb8671ffb2d24cb691b9241983ea08cf9bd 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -23,6 +23,7 @@ params.source = "dev" params.refMoVersion = "38.p6.vM25" params.refHuVersion = "38.p13.v36" params.refERCCVersion = "92" +params.seqwhoRef = "https://cloud.biohpc.swmed.edu/index.php/s/sP48taKmymSkJBM/download" params.outDir = "${baseDir}/output" params.upload = false params.email = "" @@ -67,6 +68,7 @@ repRID = params.repRID refMoVersion = params.refMoVersion refHuVersion = params.refHuVersion refERCCVersion = params.refERCCVersion +seqwhoRef = params.seqwhoRef outDir = params.outDir logsDir = "${outDir}/Logs" upload = params.upload @@ -714,6 +716,7 @@ process seqwho { tag "${repRID}" input: + val seqwhoRef path (fastq) from fastqs_seqwho val ends from endsManual_seqwho val speciesMeta from speciesMeta_seqwho @@ -734,7 +737,7 @@ process seqwho { ulimit -a >> ${repRID}.seqwho.log # get seqwho index - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download + wget -O SeqWho.ix ${seqwhoRef} echo -e "LOG: seqwho index downloaded" >> ${repRID}.seqwho.log # run seqwho