diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c02d82f55..726d92bf6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,28 +19,6 @@ concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 jobs:
-  pseudo:
-    name: Test Pseudoaligners with workflow parameters
-    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--pseudo_aligner salmon --skip_qc"
-          - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
-          - "--pseudo_aligner kallisto --skip_qc"
-          - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v4
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1.5
-
-      - name: Run pipeline with Salmon or Kallisto and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
-
   nf-test-changes:
     name: Check for changes
     runs-on: ubuntu-latest
@@ -146,7 +124,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [test, pseudo]
+    needs: [test]
     if: always()
     steps:
       - name: All tests ok
diff --git a/tests/tests/kallisto/main.nf.test b/tests/tests/kallisto/main.nf.test
new file mode 100644
index 000000000..e36b4cb9c
--- /dev/null
+++ b/tests/tests/kallisto/main.nf.test
@@ -0,0 +1,28 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../../../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Default profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
+                pseudo_aligner = 'kallisto'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            assertAll(
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") }
+            )
+        }
+    }
+}
diff --git a/tests/tests/kallisto/main.nf.test.snap b/tests/tests/kallisto/main.nf.test.snap
new file mode 100644
index 000000000..2deb6fb8d
--- /dev/null
+++ b/tests/tests/kallisto/main.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "software_versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-10T10:13:15.867122"
+    }
+}
\ No newline at end of file
diff --git a/tests/tests/salmon/main.nf.test b/tests/tests/salmon/main.nf.test
new file mode 100644
index 000000000..72f8fd4e7
--- /dev/null
+++ b/tests/tests/salmon/main.nf.test
@@ -0,0 +1,28 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../../../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Default profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
+                pseudo_aligner = 'salmon'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            assertAll(
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") }
+            )
+        }
+    }
+}
diff --git a/tests/tests/salmon/main.nf.test.snap b/tests/tests/salmon/main.nf.test.snap
new file mode 100644
index 000000000..831b1e14b
--- /dev/null
+++ b/tests/tests/salmon/main.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "software_versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-10T10:31:20.108379"
+    }
+}
\ No newline at end of file