From 962c220079ab4e10e7b9d90abd9351a9d54644df Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 17 Jun 2024 10:03:12 +0200
Subject: [PATCH] add scripts

---
 ...emote-input_s3-output_s3-work_s3-fusion.sh | 54 +++++++++++++++++++
 ...-code_remote-input_s3-output_s3-work_s3.sh |  4 +-
 ...ode_local-input_s3-output_s3-work_local.sh | 32 +++++++++++
 ...l-code_local-input_s3-output_s3-work_s3.sh | 51 ++++++++++++++++++
 ...-code_remote-input_s3-output_s3-work_s3.sh |  2 +-
 5 files changed, 140 insertions(+), 3 deletions(-)
 create mode 100755 scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh
 create mode 100755 scripts/run_local-code_local-input_s3-output_s3-work_local.sh
 create mode 100755 scripts/run_local-code_local-input_s3-output_s3-work_s3.sh

diff --git a/scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh b/scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh
new file mode 100755
index 0000000..580e591
--- /dev/null
+++ b/scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh
@@ -0,0 +1,54 @@
+#!/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
+
+# 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 = 'di_compute'
+    container = 'bash:4.0'
+}
+
+aws {
+    region = 'eu-west-1'
+    batch {
+        cliPath = '/home/ec2-user/miniconda/bin/aws'
+    }
+}
+EOF
+
+
+NXF_VER=23.10.1 nextflow run \
+  viash-io/test-nextflow-wave-fusion \
+  -r main_build \
+  -main-script target/nextflow/method/main.nf \
+  -profile docker \
+  -w $WORK \
+  -c $NXF_CONFIG \
+  -latest \
+  --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"
diff --git a/scripts/run_batch-code_remote-input_s3-output_s3-work_s3.sh b/scripts/run_batch-code_remote-input_s3-output_s3-work_s3.sh
index 0f66b23..36a3186 100755
--- a/scripts/run_batch-code_remote-input_s3-output_s3-work_s3.sh
+++ b/scripts/run_batch-code_remote-input_s3-output_s3-work_s3.sh
@@ -20,7 +20,7 @@ echo "Running component"
 cat > $NXF_CONFIG <<EOF
 process {
     executor = 'awsbatch'
-    queue = 'di_compute'
+    queue = 'nextflow_queue_nofusion'
     container = 'bash:4.0'
 }
 
@@ -33,7 +33,7 @@ aws {
 EOF
 
 
-NXF_VER=23.10.0 nextflow run \
+NXF_VER=23.10.1 nextflow run \
   viash-io/test-nextflow-wave-fusion \
   -r main_build \
   -main-script target/nextflow/method/main.nf \
diff --git a/scripts/run_local-code_local-input_s3-output_s3-work_local.sh b/scripts/run_local-code_local-input_s3-output_s3-work_local.sh
new file mode 100755
index 0000000..a7915c5
--- /dev/null
+++ b/scripts/run_local-code_local-input_s3-output_s3-work_local.sh
@@ -0,0 +1,32 @@
+#!/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
+
+# clear output dir
+echo "Clearing output directory"
+aws s3 rm $TMPOUT --recursive
+[ -d "$OUT" ] && rm -r "$OUT"
+
+# run component
+echo "Running component"
+NXF_VER=23.10.1 nextflow run \
+  . \
+  -main-script target/nextflow/method/main.nf \
+  -profile docker \
+  -latest \
+  --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"
diff --git a/scripts/run_local-code_local-input_s3-output_s3-work_s3.sh b/scripts/run_local-code_local-input_s3-output_s3-work_s3.sh
new file mode 100755
index 0000000..ff3ec5b
--- /dev/null
+++ b/scripts/run_local-code_local-input_s3-output_s3-work_s3.sh
@@ -0,0 +1,51 @@
+#!/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
+
+# clear output dir
+echo "Clearing output directory"
+aws s3 rm $TMPOUT --recursive
+[ -d "$OUT" ] && rm -r "$OUT"
+
+echo "aws profile: $AWS_PROFILE"
+
+# create config
+cat > $NXF_CONFIG <<EOF
+fusion {
+    enabled = true
+    exportStorageCredentials = true
+}
+
+wave {
+    enabled = true
+}
+EOF
+
+
+# run component
+echo "Running component"
+NXF_VER=23.10.1 nextflow run \
+  . \
+  -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"
diff --git a/scripts/run_local-code_remote-input_s3-output_s3-work_s3.sh b/scripts/run_local-code_remote-input_s3-output_s3-work_s3.sh
index e0076f7..48e9b0b 100755
--- a/scripts/run_local-code_remote-input_s3-output_s3-work_s3.sh
+++ b/scripts/run_local-code_remote-input_s3-output_s3-work_s3.sh
@@ -29,7 +29,7 @@ EOF
 
 # run component
 echo "Running component"
-NXF_VER=23.10.0 nextflow run \
+NXF_VER=23.10.1 nextflow run \
   viash-io/test-nextflow-wave-fusion \
   -r main_build \
   -main-script target/nextflow/method/main.nf \