From ff2d89db88a74f3af53840dc03093d7e3cc39166 Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
Date: Wed, 19 Oct 2022 10:16:36 +0200
Subject: [PATCH 1/2] enforce julia version

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 0342fb0..34bc587 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM julia
+FROM julia:1.8.0-bullseye
 
 ADD Project.toml /tool/
 ADD components /tool/components

From 6cff989845e95b93f6d4a690b3e5f3a0e7829f5a Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
Date: Wed, 19 Oct 2022 10:16:46 +0200
Subject: [PATCH 2/2] make sure the check (and other) failures get forwarded
 correctly

---
 run_pipeline.sh | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/run_pipeline.sh b/run_pipeline.sh
index 599b192..3e86916 100755
--- a/run_pipeline.sh
+++ b/run_pipeline.sh
@@ -22,11 +22,16 @@ DOCKER="docker run --rm $MOUNT $IMAGE julia --project "
 mkdir -p output logs
 export RESTIMATOR_OUTDIR=output
 
-if $DOCKER components/check_input.jl "$FILE"
+$DOCKER components/check_input.jl "$FILE" 2>&1 | log check
+if [ ${PIPESTATUS[0]} -eq 0 ]
 then
+	st=0
 	$DOCKER components/estimate_r_t.jl "$FILE" 2>&1 | log rt
+	[ ${PIPESTATUS[0]} -eq 0 ] || st=1
 	$DOCKER components/estimate_r_eff.jl "$FILE" 2>&1 | log reff
+	[ ${PIPESTATUS[0]} -eq 0 ] || st=1
+	exit $st
 else
 	echo $0: check failed >&2
 	exit 1
-fi 2>&1 | log check
+fi