From 26363f5b7832b6877de159b8de0571f42477a7a9 Mon Sep 17 00:00:00 2001 From: Felix Rios Date: Wed, 23 Feb 2022 16:13:48 +0100 Subject: [PATCH] Fixed bug with GOBNILP online estimate on timeout. --- workflow/rules/algorithm_shell_commands.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/rules/algorithm_shell_commands.smk b/workflow/rules/algorithm_shell_commands.smk index d7206997..e7ac1374 100644 --- a/workflow/rules/algorithm_shell_commands.smk +++ b/workflow/rules/algorithm_shell_commands.smk @@ -178,8 +178,8 @@ def alg_shell(algorithm): echo -e gobnilp/scoring/prune = {wildcards.prune} >> {output.adjmat}.gobnilp.set echo -e gobnilp/delimiter = \134\042,\134\042 >> {output.adjmat}.gobnilp.set cat resources/extra_args/{wildcards.extra_args} >> {output.adjmat}.gobnilp.set - if [ {wildcards.timeout} != \"None\" ]; then - timeout --signal=SIGKILL {wildcards.timeout} bash -c '/myappdir/gobnilp/bin/gobnilp -f=dat -g={output.adjmat}.gobnilp.set {input.data}'; + if [ {wildcards.timeout} != \"None\" ]; then + (timeout --signal=SIGKILL {wildcards.timeout} bash -c '/myappdir/gobnilp/bin/gobnilp -f=dat -g={output.adjmat}.gobnilp.set {input.data}' || exit 0) else /myappdir/gobnilp/bin/gobnilp -f=dat -g={output.adjmat}.gobnilp.set {input.data}; fi