From 1ec25cbbd039a9df4521328f6402bf1589827f98 Mon Sep 17 00:00:00 2001
From: ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Mon, 25 Nov 2019 17:22:25 +0100
Subject: [PATCH] add line to rule strphlan_clade_profiling to handle errors
when executing strainphlan_ggtree.R
---
rules/phlanprof.smk | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/rules/phlanprof.smk b/rules/phlanprof.smk
index 150b136..d25dac3 100644
--- a/rules/phlanprof.smk
+++ b/rules/phlanprof.smk
@@ -305,7 +305,8 @@ rule strphlan_clade_profiling:
{input.samples_metadata} \
{output.clade_result_dir}/{wildcards.clade}.fasta \
{output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_1.png \
- {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_2.png; fi') &>{log}
+ {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_2.png || \
+ echo "strainphlan_ggtree.R halted with non-zero exit status!"; fi') &>{log}
'''
def aggregate_clade_profiles(wildcards):
--
GitLab