From 39fab8dd531813b9430b94452f9b19bb20586594 Mon Sep 17 00:00:00 2001
From: Magnus Wahlberg <endast@gmail.com>
Date: Fri, 24 May 2024 13:52:44 +0200
Subject: [PATCH] Post run cmd in pipeline tests (#100)

* Add postrun_cmd

* test post run

* Update run-pipeline.yml

* Update run-pipeline.yml

* Update run-pipeline.yml

* Update pipeline-tests.yml

* Update pipeline-tests.yml

* Remove samples
---
 .github/workflows/run-pipeline.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/run-pipeline.yml b/.github/workflows/run-pipeline.yml
index e5020d1d..6971a7fd 100644
--- a/.github/workflows/run-pipeline.yml
+++ b/.github/workflows/run-pipeline.yml
@@ -34,6 +34,9 @@ on:
       fasta_download_path:
         required: false
         type: string
+      postrun_cmd:
+        required: false
+        type: string
 
 jobs:
   Run-Pipeline:
@@ -78,3 +81,7 @@ jobs:
             ${{ (endsWith(inputs.pipeline_config, 'ml') && '--configfile')  || '' }}  ${{ inputs.pipeline_config }} \
             --snakefile ${{inputs.pipeline_file}} --show-failed-logs -F
           shell: micromamba-shell {0}
+        - name: Run post pipeline cmd
+          if: inputs.postrun_cmd
+          run: ${{inputs.postrun_cmd}}
+          shell: micromamba-shell {0}