From bf96062e51603df43f4bfc22d1a417ac03d49332 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Fri, 7 Sep 2018 11:13:00 -0500 Subject: [PATCH] Revert and add outputs for genome param and ref to error exit output --- workflow/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/main.nf b/workflow/main.nf index 96336fa..f3f3fca 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -8,7 +8,7 @@ params.fastq = "$baseDir/../test_data/*.fastq.gz" params.designFile = "$baseDir/../test_data/design.csv" params.genome = 'GRCh38' params.genomes = [] -params.ref = params.genome ? params.genomes[ ${params.genome} ].ref ?: false : false +params.ref = params.genome ? params.genomes[ params.genome ].ref ?: false : false params.expectCells = 10000 params.forceCells = 0 @@ -18,7 +18,7 @@ if( params.ref ){ .fromPath(params.ref) .ifEmpty { exit 1, "referene not found: ${params.ref}" } } else { - exit 1, "No reference genome specified." + exit 1, "No reference genome specified. ${params.genome} ${params.ref}" } // Define List of Files -- GitLab