From 77809b53ad98ac8a4ad9b42375e59d66b6fd62a8 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 17 Jun 2024 10:38:38 +0200
Subject: [PATCH] add initial tw script

---
 ...-code_remote-input_s3-output_s3-work_s3.sh | 62 +++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100755 scripts/run_tw-code_remote-input_s3-output_s3-work_s3.sh

diff --git a/scripts/run_tw-code_remote-input_s3-output_s3-work_s3.sh b/scripts/run_tw-code_remote-input_s3-output_s3-work_s3.sh
new file mode 100755
index 0000000..9db4ea1
--- /dev/null
+++ b/scripts/run_tw-code_remote-input_s3-output_s3-work_s3.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+set -e
+
+script_name=$(basename "$0")
+TMPOUT=s3://data-intuitive-tmp/test-nextflow-wave-fusion/output/${script_name%.sh}
+OUT=output/${script_name%.sh}
+RES=s3://data-intuitive-tmp/test-nextflow-wave-fusion/resources
+WORK=s3://data-intuitive-tmp/test-nextflow-wave-fusion/work/${script_name%.sh}
+NXF_CONFIG=/tmp/${script_name%.sh}.config
+PARAMS=/tmp/${script_name%.sh}.yaml
+
+# set aws profile
+export AWS_PROFILE=di
+echo "aws profile: $AWS_PROFILE"
+
+# clear output dir
+echo "Clearing output directory"
+aws s3 rm $TMPOUT --recursive
+[ -d "$OUT" ] && rm -r "$OUT"
+
+# run component
+echo "Running component"
+
+cat > $NXF_CONFIG <<EOF
+process {
+    executor = 'awsbatch'
+    queue = 'nextflow_queue_nofusion'
+    container = 'bash:4.0'
+}
+
+aws {
+    region = 'eu-west-1'
+    batch {
+        cliPath = '/home/ec2-user/miniconda/bin/aws'
+    }
+}
+EOF
+
+cat > $PARAMS <<EOF
+input: $RES/input1.txt
+multiple_input: "$RES/input1.txt;$RES/input2.txt"
+publish_dir: "$TMPOUT"
+EOF
+
+tw launch \
+  viash-io/test-nextflow-wave-fusion \
+  --revision main_build \
+  --main-script target/nextflow/method/main.nf \
+  --work-dir $WORK \
+  --workspace XXX \
+  --compute-env YYY \
+  --config $NXF_CONFIG \
+  --params-file $PARAMS
+
+# sync output
+echo "Syncing output"
+aws s3 sync $TMPOUT $OUT
+
+# check if output is correct
+echo "Checking output"
+scripts/verify_output.sh "$OUT"