From 0a0dffa37ca581386d17cb9dd4296e18697196f4 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Sun, 4 Dec 2022 12:06:33 +0100
Subject: [PATCH] Try separating MALT

---
 .github/workflows/ci.yml | 33 +++++++++++++++++++++++++++++++++
 conf/test.config         |  2 +-
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d179c6e..dad2838 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -134,3 +134,36 @@ jobs:
         with:
           command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
           attempt_limit: 3
+
+  malt:
+    name: Test MALT with workflow parameters
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "21.10.3"
+          - "latest-everything"
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Show current locale
+        run: locale
+
+      - name: Set UTF-8 enabled locale
+        run: |
+          sudo locale-gen en_US.UTF-8
+          sudo update-locale LANG=en_US.UTF-8
+
+      - name: Run pipeline with test data
+        uses: Wandalen/wretry.action@v1.0.11
+        with:
+          command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --outdir ./results
+          attempt_limit: 3
diff --git a/conf/test.config b/conf/test.config
index 898743e..db9f81d 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -35,7 +35,7 @@ params {
     run_kaiju                             = true
     run_kraken2                           = true
     run_bracken                           = true
-    run_malt                              = true
+    run_malt                              = false
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true