From 39136947c3d1b59637730240c8eee63d1cc07d49 Mon Sep 17 00:00:00 2001 From: Cassie Litchfield Date: Tue, 4 Jun 2024 15:42:24 +0200 Subject: [PATCH] symlink specific gridss index files genome_gridss_index folder may contain additional files that are staged by nextflow if they are part of the inputs (e.g. someone might have the .dict file in this folder if they created it via gridss.PrepareReference). This causes an error when we try to symlink the entire contents of the folder. Could we change this line to symlink the specific files of interest? --- modules/local/virusbreakend/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf index d31aa98f..6ec6438a 100644 --- a/modules/local/virusbreakend/main.nf +++ b/modules/local/virusbreakend/main.nf @@ -29,7 +29,7 @@ process VIRUSBREAKEND { """ # Symlink indices next to assembly FASTA - ln -s \$(find -L ${genome_gridss_index} -type f) ./ + ln -s \$(find -L ${genome_gridss_index} -type f -name *.gridsscache -o -name *.img) ./ virusbreakend \\ ${args} \\