From 676d5303c00ee01cfa1d5e0ee8a7b3b7790d4bd7 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 17 Jun 2024 13:00:04 +0200
Subject: [PATCH] add input scripts

---
 ...ut_s3-output_s3-work_s3_nxf24042_vsh075.sh | 57 +++++++++++++++++++
 ...ut_s3-output_s3-work_s3_nxf24042_vsh085.sh | 57 +++++++++++++++++++
 2 files changed, 114 insertions(+)
 create mode 100755 scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh075.sh
 create mode 100755 scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh085.sh

diff --git a/scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh075.sh b/scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh075.sh
new file mode 100755
index 0000000..2dcde4b
--- /dev/null
+++ b/scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh075.sh
@@ -0,0 +1,57 @@
+#!/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
+
+# 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"
+
+# create config
+cat > $NXF_CONFIG <<'EOF'
+fusion {
+    enabled = true
+}
+
+wave {
+    enabled = true
+}
+
+docker {
+  runOptions = '-v $HOME/.aws/credentials:/credentials -e AWS_SHARED_CREDENTIALS_FILE=/credentials -e AWS_PROFILE=$AWS_PROFILE'
+}
+EOF
+
+
+# run component
+echo "Running component"
+NXF_VER=24.04.2 nextflow run \
+  viash-io/test-nextflow-wave-fusion \
+  -r build_0_7_5 \
+  -main-script target/nextflow/method/main.nf \
+  -profile docker \
+  -latest \
+  -w $WORK \
+  -c $NXF_CONFIG \
+  --input $RES/input1.txt \
+  --multiple_input "$RES/input2.txt" \
+  --publish_dir "$TMPOUT"
+
+# sync output
+echo "Syncing output"
+aws s3 sync $TMPOUT $OUT
+
+# check if output is correct
+echo "Checking output"
+scripts/verify_output.sh "$OUT"
diff --git a/scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh085.sh b/scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh085.sh
new file mode 100755
index 0000000..0a2e8bc
--- /dev/null
+++ b/scripts/run_local-code_remote-input_s3-output_s3-work_s3_nxf24042_vsh085.sh
@@ -0,0 +1,57 @@
+#!/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
+
+# 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"
+
+# create config
+cat > $NXF_CONFIG <<'EOF'
+fusion {
+    enabled = true
+}
+
+wave {
+    enabled = true
+}
+
+docker {
+  runOptions = '-v $HOME/.aws/credentials:/credentials -e AWS_SHARED_CREDENTIALS_FILE=/credentials -e AWS_PROFILE=$AWS_PROFILE'
+}
+EOF
+
+
+# run component
+echo "Running component"
+NXF_VER=24.04.2 nextflow run \
+  viash-io/test-nextflow-wave-fusion \
+  -r build_0_8_5 \
+  -main-script target/nextflow/method/main.nf \
+  -profile docker \
+  -latest \
+  -w $WORK \
+  -c $NXF_CONFIG \
+  --input $RES/input1.txt \
+  --multiple_input "$RES/input1.txt;$RES/input2.txt" \
+  --publish_dir "$TMPOUT"
+
+# sync output
+echo "Syncing output"
+aws s3 sync $TMPOUT $OUT
+
+# check if output is correct
+echo "Checking output"
+scripts/verify_output.sh "$OUT"