From 906d61001c0e2ceed0629783cf2a079ecfc36a21 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 19 Nov 2020 17:54:17 +0000 Subject: [PATCH 1/2] Initialise args for umitools extract --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index efc64a10d..1186daf97 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -52,6 +52,7 @@ params { publish_files = ['txt':'', 'html':'fastqc', 'zip':'fastqc'] } 'umitools_extract' { + args = "" publish_files = ['log':''] } 'sortmerna' { From a84b4c88462d566f937a7db6e40fcf19b2853dcc Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 23 Nov 2020 14:21:45 +0000 Subject: [PATCH 2/2] Change genome wording --- rnaseq.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rnaseq.nf b/rnaseq.nf index 255087238..b0695e667 100755 --- a/rnaseq.nf +++ b/rnaseq.nf @@ -13,7 +13,7 @@ params.summary_params = [:] */ // Check if genome exists in the config file if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}" + exit 1, "Genome '${params.genome}' was not found in any config files made available to the pipeline. Currently, the available genomes are ${params.genomes.keySet().join(", ")}" } // Auto-load genome files from genome config