update scripts & add placeholder nf and config

viash-io · Mar 21, 2024 · 2585032 · 2585032
1 parent 4034fdd
commit 2585032
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Showing 4 changed files with 25 additions and 5 deletions.
diff --git a/main.nf b/main.nf
diff --git a/nextflow.config b/nextflow.config
diff --git a/scripts/run_local.sh b/scripts/run_local.sh
@@ -2,11 +2,10 @@
 
 set -e
 
-# build component
-rm -r target && viash ns build --parallel --setup cb
+OUT=output/local
 
 # clear output dir
-rm -r output/local
+rm -r "$OUT"
 
 # run component
 NXF_VER=23.10.0 nextflow run \
@@ -15,7 +14,7 @@ NXF_VER=23.10.0 nextflow run \
   -profile docker \
   --input resources/input1.txt \
   --multiple_input "resources/input1.txt;resources/input2.txt" \
-  --publish_dir output/local
+  --publish_dir "$OUT"
 
 # check if output is correct
-scripts/verify_output.sh output/local
+scripts/verify_output.sh "$OUT"
diff --git a/scripts/run_local_with_remote.sh b/scripts/run_local_with_remote.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -e
+
+OUT=output/local_with_remote
+
+# clear output dir
+rm -r "$OUT"
+
+# run component
+NXF_VER=23.10.0 nextflow run \
+  viash-io/test-nextflow-wave-fusion \
+  -r main_build \
+  -main-script target/nextflow/method/main.nf \
+  -profile docker \
+  --input resources/input1.txt \
+  --multiple_input "resources/input1.txt;resources/input2.txt" \
+  --publish_dir "$OUT"
+
+# check if output is correct
+scripts/verify_output.sh "$OUT"