From 665a1380d4a58989d5450cf82bede116ac67d064 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 12 Nov 2026 15:48:58 -0600
Subject: [PATCH] Make AWS full tests use verified S3 inputs

Pin Nextflow 26.10.5 so connection-reset staging failures can retry.
Use the checksum-validated private mirror for AWS tests while leaving
public ENA samplesheets unchanged for other users.

Migrate to the supported Seqera launch action to select the remote
runtime explicitly and wait for the final workflow result. Preserve a
launch-result artifact on success or failure.
---
 .github/workflows/awsfulltest.yml | 36 +++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 1f4d5a8..32705db 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -23,14 +23,18 @@ jobs:
           echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
+        id: launch
+        uses: seqeralabs/action-seqera-launch@f7b1a39afc8bb65f58b84150cd214b33fe416fef
         with:
-          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
+          workspace-id: ${{ vars.TOWER_WORKSPACE_ID }}
+          access-token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute-env: ${{ vars.TOWER_COMPUTE_ENV }}
+          nextflow-version: 26.10.5
+          syntax-parser: v2
+          wait: completion
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/deepmutscan/work-${{ steps.revision.outputs.revision }}
-          nextflow_config: |
+          work-dir: s3://${{ vars.AWS_S3_BUCKET }}/work/deepmutscan/work-${{ steps.revision.outputs.revision }}
+          nextflow-config: |
             plugins {
               id 'nf-slack@0.5.0'
               id 'nf-schema@2.7.2'
@@ -53,13 +57,23 @@ jobs:
             }
           parameters: |
             {
-              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/deepmutscan/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/deepmutscan/results-${{ steps.revision.outputs.revision }}",
+              "input": "s3://${{ vars.AWS_S3_BUCKET }}/test-data/deepmutscan/PRJEB110196/GID1A_full.csv"
             }
           profiles: test_full
 
+      - name: Save Seqera Platform launch result
+        if: always() && steps.launch.outputs.workflow-id != ''
+        env:
+          SEQERA_WORKFLOW_ID: ${{ steps.launch.outputs.workflow-id }}
+          SEQERA_WORKFLOW_URL: ${{ steps.launch.outputs.workflow-url }}
+          SEQERA_WORKFLOW_STATUS: ${{ steps.launch.outputs.status }}
+          SEQERA_WORKFLOW_ERROR: ${{ steps.launch.outputs.error-message }}
+        run: |
+          jq -n '{workflowId: env.SEQERA_WORKFLOW_ID, workflowUrl: env.SEQERA_WORKFLOW_URL, status: env.SEQERA_WORKFLOW_STATUS, errorMessage: env.SEQERA_WORKFLOW_ERROR}' > seqera-launch.json
+
       - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        if: always() && steps.launch.outputs.workflow-id != ''
         with:
-          name: Seqera Platform debug log file
-          path: |
-            tower_action_*.log
-            tower_action_*.json
+          name: Seqera Platform launch result
+          path: seqera-launch.json