From bff8c6cde7c0e7039ab4a1753402c47e82e06b9e Mon Sep 17 00:00:00 2001 From: dmc2245 Date: Fri, 23 Aug 2024 10:48:03 -0400 Subject: [PATCH] annovar in pixi+mamba --- variant-annotation/annovar-rap.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/variant-annotation/annovar-rap.ipynb b/variant-annotation/annovar-rap.ipynb index 46e379d..f331d1f 100644 --- a/variant-annotation/annovar-rap.ipynb +++ b/variant-annotation/annovar-rap.ipynb @@ -247,7 +247,7 @@ "parameter: mem = \"30G\"\n", "# Load annovar module from cluster\n", "parameter: annovar_module = '''\n", - "module load ANNOVAR/2020Jun08-foss-2018b-Perl-5.28.0\n", + "module load Annovar/202004\n", "echo \"Module annovar loaded\"\n", "{cmd}\n", "'''\n", @@ -569,7 +569,7 @@ "parameter: x_ref = path(f\"{xref_path}/mart_export_2021_LOFtools.txt\")\n", "output: f'{cwd}/{_input:bn}.{build}_multianno.csv'\n", "task: trunk_workers = 1, walltime = walltime, mem = mem, cores = numThreads, tags = f'{step_name}_{_output:bn}', template = '{cmd}' if executable('annotate_variation.pl').target_exists() else annovar_module\n", - "bash: container=container_annovar, volumes=[f'{humandb:a}:{humandb:a}', f'{x_ref:ad}:{x_ref:ad}'], expand=\"${ }\", stderr=f'{_output:n}.err', stdout=f'{_output:n}.out'\n", + "bash: expand=\"${ }\", stderr=f'{_output:n}.err', stdout=f'{_output:n}.out'\n", " #do not add -intronhgvs as option -> writes cDNA variants as HGVS but creates issues (+2 splice site reported only)\n", " #-nastring . can only be . for VCF files\n", " #regsnpintron might cause shifted lines (be carefull using)\n",