diff --git a/.github/workflows/ci-changes.yml b/.github/workflows/ci-changes.yml
new file mode 100644
index 000000000..398f7d312
--- /dev/null
+++ b/.github/workflows/ci-changes.yml
@@ -0,0 +1,85 @@
+name: nf-test on changes
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  pull_request:
+    branches:
+      - dev
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/tags.yml"
+
+  test_changes:
+    name: ${{ matrix.tags }} ${{ matrix.component }} ${{ matrix.profile }}
+    runs-on: ubuntu-20.04
+    needs: changes
+    if: needs.changes.outputs.tags != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile: ["docker"] # TODO Add singularity/conda
+        component: ["pipeline"] # TODO , "subworkflows", "modules"]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      - name: Run nf-test
+        run: nf-test test --profile=${{ matrix.profile }} tests/${{ matrix.component }}/${{ matrix.tags }}/*.nf.test --junitxml=${{ matrix.tags }}.xml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "${{ matrix.tags }}.xml"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d71cadb70..1c4fdb8fc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,10 +1,9 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
+  pull_request:
     branches:
       - dev
-  pull_request:
   release:
     types: [published]
 
@@ -13,7 +12,7 @@ env:
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: Run ${{ matrix.profile }}-${{ matrix.NXF_VER }} pipeline test
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
     runs-on: ubuntu-latest
@@ -22,113 +21,56 @@ jobs:
         NXF_VER:
           - "21.10.3"
           - "latest-everything"
+        test:
+          - "default"
+        profile: ["docker"]
+        exclude:
+          - NXF_VER: "latest-everything"
+            profile: "conda"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-  star_salmon:
-    name: Test STAR Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--skip_trimming"
-          - "--gtf false"
-          - "--star_index false"
-          - "--transcript_fasta false"
-          - "--min_mapped_reads 90"
-          - "--with_umi"
-          - "--with_umi --skip_trimming"
-          - "--remove_ribo_rna --skip_qualimap"
-          - "--bam_csi_index"
-          - "--save_align_intermeds --save_reference"
-          - "--featurecounts_group_type false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with STAR and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
-
-  star_rsem:
-    name: Test STAR RSEM with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--rsem_index false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with RSEM STAR and various parameters
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
 
-  hisat2:
-    name: Test HISAT2 with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--hisat2_index false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
 
-      - name: Run pipeline with HISAT2 and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
 
-  salmon:
-    name: Test Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc --skip_alignment"
-          - "--salmon_index false --transcript_fasta false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Run nf-test
+        run: nf-test test --profile=${{ matrix.profile }} tests/pipeline/default/*.nf.test --junitxml=default.xml
 
-      - name: Run pipeline with Salmon and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "default.xml"
diff --git a/.gitignore b/.gitignore
index 5124c9ac7..089a40797 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test
diff --git a/.nf-core.yml b/.nf-core.yml
index 40bcac74d..ca3842aeb 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -4,3 +4,4 @@ lint:
     - assets/email_template.html
     - assets/email_template.txt
     - lib/NfcoreTemplate.groovy
+  actions_ci: False
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ad658113..d5375a7c7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 - Update modules to latest restructuring on nf-core/modules
+- [[#883](https://github.com/nf-core/rnaseq/pull/883)] - Migrate CI tests to nf-test
 
 ### Parameters
 
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 000000000..703b5a4ec
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "conf/test.config"
+    // profile "docker"
+
+}
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
new file mode 100644
index 000000000..3cd8ab3cb
--- /dev/null
+++ b/tests/config/nextflow.config
@@ -0,0 +1,38 @@
+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    enable_conda = false
+    singularity_pull_docker_container = false
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
+}
+
+process {
+  cpus = 2
+  memory = 6.GB
+  time = 48.h
+}
+
+if ("$PROFILE" == "singularity") {
+    singularity.enabled = true
+    singularity.autoMounts = true
+} else if ("$PROFILE" == "conda") {
+    params.enable_conda = true
+} else {
+    docker.enabled = true
+    docker.runOptions = '-u \$(id -u):\$(id -g)'
+}
+
+// Load test_data.config containing paths to test data
+includeConfig 'test_data.config'
+
+// Load default nextflow.config for default module params
+includeConfig '../../nextflow.config'
+
+// Load modules.config for default module params
+includeConfig '../../conf/modules.config'
+
+manifest {
+  nextflowVersion = '!>=21.04.0'
+}
diff --git a/tests/config/tags.yml b/tests/config/tags.yml
new file mode 100644
index 000000000..0ff8e8ab9
--- /dev/null
+++ b/tests/config/tags.yml
@@ -0,0 +1,48 @@
+# quantify_salmon:
+#   - subworkflows/local/quantify_salmon.nf
+#   - tests/subworkflows/local/quantify_salmon/**
+#   - modules/nf-core/software/salmon/quant/**
+#   - modules/local/salmon_tx2gene.nf
+#   - modules/local/salmon_tximport.nf
+#   - modules/local/salmon_merge_counts.nf
+#   - modules/local/salmon_summarizedexperiment.nf
+
+hisat2:
+  - modules/nf-core/hisat2/**
+  - subworkflows/nf-core/align_hisat2.nf
+  - tests/pipeline/hisat2/**
+
+# quantify_rsem:
+#   - subworkflows/local/quantify_rsem.nf
+#   - subworkflows/nf-core/bam_sort_samtools.nf
+#   - tests/subworkflows/local/quantify_rsem/**
+#   - modules/nf-core/software/rsem/calculateexpression/**
+#   - modules/local/rsem_merge_counts.nf
+
+salmon:
+  - bin/salmon_summarizedexperiment.r
+  - bin/salmon_tx2gene.py
+  - bin/salmon_tximport.r
+  - modules/local/salmon_summarizedexperiment.nf
+  - modules/local/salmon_tx2gene.nf
+  - modules/local/salmon_tximport.nf
+  - modules/nf-core/salmon/**
+  - subworkflows/local/quantify_salmon.nf
+  - tests/pipeline/salmon/**
+  # - tests/subworkflows/local/quantify_salmon/
+
+star_salmon:
+  - modules/local/star_align_igenomes.nf
+  - modules/local/star_genomegenerate_igenomes.nf
+  - modules/nf-core/star/**
+  - subworkflows/local/align_star.nf
+  - tests/pipeline/star_salmon/**
+
+star_rsem:
+  - bin/prepare-for-rsem.py
+  - modules/local/rsem_merge_counts.nf
+  - modules/local/umitools_prepareforrsem.nf
+  - modules/nf-core/rsem/**
+  - subworkflows/local/quantify_rsem.nf
+  - tests/pipeline/star_rsem/**
+  # - tests/subworkflows/local/quantify_rsem/
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
new file mode 100644
index 000000000..0d7304b12
--- /dev/null
+++ b/tests/config/test_data.config
@@ -0,0 +1,3 @@
+def nf_core_rnaseq_data = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/data/"
+
+includeConfig 'https://github.com/nf-core/modules/raw/master/tests/config/test_data.config'
diff --git a/tests/modules/samplesheet_check/main.nf.test b/tests/modules/samplesheet_check/main.nf.test
new file mode 100644
index 000000000..4e5ef97fa
--- /dev/null
+++ b/tests/modules/samplesheet_check/main.nf.test
@@ -0,0 +1,19 @@
+nextflow_process {
+    name "samplesheet_check"
+    script "modules/local/samplesheet_check.nf"
+    process "SAMPLESHEET_CHECK"
+
+    test("Should run without failure") {
+        when {
+            process {
+                """
+                input[0] = file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+        }
+    }
+}
diff --git a/tests/pipeline/default/main.nf.test b/tests/pipeline/default/main.nf.test
new file mode 100644
index 000000000..1d01b4abd
--- /dev/null
+++ b/tests/pipeline/default/main.nf.test
@@ -0,0 +1,69 @@
+nextflow_pipeline {
+
+    name "default"
+    script "main.nf"
+
+    test("default test config") {
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 197
+
+            assert new File("$outputDir/salmon/salmon.merged.gene_counts_length_scaled.rds")
+            assert new File("$outputDir/salmon/salmon.merged.gene_counts_length_scaled.tsv")
+            assert new File("$outputDir/salmon/salmon.merged.gene_counts.rds")
+            assert new File("$outputDir/salmon/salmon.merged.gene_counts_scaled.rds")
+            assert new File("$outputDir/salmon/salmon.merged.gene_counts_scaled.tsv")
+            assert new File("$outputDir/salmon/salmon.merged.gene_counts.tsv")
+            assert new File("$outputDir/salmon/salmon.merged.gene_tpm.tsv")
+            assert new File("$outputDir/salmon/salmon.merged.transcript_counts.rds")
+            assert new File("$outputDir/salmon/salmon.merged.transcript_counts.tsv")
+            assert new File("$outputDir/salmon/salmon.merged.transcript_tpm.tsv")
+
+            assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_1_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_1_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_2_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/RAP1_IAA_30M_REP1_2_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP1_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP1_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP2_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/RAP1_UNINDUCED_REP2_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/WT_REP1_1_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/WT_REP1_1_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/WT_REP1_2_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/WT_REP1_2_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/WT_REP2_1_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/WT_REP2_1_fastqc.zip").exists()
+            assert new File("$outputDir/fastqc/WT_REP2_2_fastqc.html").exists()
+            assert new File("$outputDir/fastqc/WT_REP2_2_fastqc.zip").exists()
+
+            assert new File("$outputDir/multiqc/star_salmon/multiqc_report.html").exists()
+
+            assert new File("$outputDir/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").exists()
+            assert new File("$outputDir/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").exists()
+            assert new File("$outputDir/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").exists()
+            assert new File("$outputDir/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").exists()
+            assert new File("$outputDir/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").exists()
+            assert new File("$outputDir/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").exists()
+            assert new File("$outputDir/star_salmon/WT_REP1.markdup.sorted.bam").exists()
+            assert new File("$outputDir/star_salmon/WT_REP1.markdup.sorted.bam.bai").exists()
+            assert new File("$outputDir/star_salmon/WT_REP2.markdup.sorted.bam").exists()
+            assert new File("$outputDir/star_salmon/WT_REP2.markdup.sorted.bam.bai").exists()
+
+            assert new File("$outputDir/trimgalore/RAP1_IAA_30M_REP1_1.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/RAP1_IAA_30M_REP1_2.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/RAP1_UNINDUCED_REP1.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/RAP1_UNINDUCED_REP2.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/WT_REP1_1.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/WT_REP1_2.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/WT_REP2_1.fastq.gz_trimming_report.txt").exists()
+            assert new File("$outputDir/trimgalore/WT_REP2_2.fastq.gz_trimming_report.txt").exists()
+        }
+    }
+
+}
diff --git a/tests/pipeline/hisat2/main.nf.test b/tests/pipeline/hisat2/main.nf.test
new file mode 100644
index 000000000..109944dd8
--- /dev/null
+++ b/tests/pipeline/hisat2/main.nf.test
@@ -0,0 +1,38 @@
+nextflow_pipeline {
+
+    name "hisat2"
+    script "main.nf"
+
+    test("with skip_qc workflow parameters") {
+        when {
+            params {
+                aligner = "hisat2"
+                skip_qc = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 120
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with hisat2_index false workflow parameters") {
+        when {
+            params {
+                aligner = "hisat2"
+                hisat2_index = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 186
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+}
diff --git a/tests/pipeline/salmon/main.nf.test b/tests/pipeline/salmon/main.nf.test
new file mode 100644
index 000000000..700d219f6
--- /dev/null
+++ b/tests/pipeline/salmon/main.nf.test
@@ -0,0 +1,40 @@
+nextflow_pipeline {
+
+    name "Salmon"
+    script "main.nf"
+
+    test("with skip_qc skip_alignment workflow parameters") {
+        when {
+            params {
+                pseudo_aligner = "salmon"
+                skip_qc = true
+                skip_alignment = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 33
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with salmon_index false transcript_fasta false workflow parameters") {
+        when {
+            params {
+                pseudo_aligner = "salmon"
+                salmon_index = false
+                transcript_fasta = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 199
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+}
diff --git a/tests/pipeline/star_rsem/main.nf.test b/tests/pipeline/star_rsem/main.nf.test
new file mode 100644
index 000000000..ce00fa8e7
--- /dev/null
+++ b/tests/pipeline/star_rsem/main.nf.test
@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "STAR RSEM"
+    script "main.nf"
+
+    test("with skip_qc workflow parameters") {
+        when {
+            params {
+                aligner = "star_rsem"
+                skip_qc = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 120
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with rsem_index false workflow parameters") {
+        when {
+            params {
+                pseudo_aligner = "salmon"
+                aligner = "star_rsem"
+                rsem_index = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 187
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+}
diff --git a/tests/pipeline/star_salmon/main.nf.test b/tests/pipeline/star_salmon/main.nf.test
new file mode 100644
index 000000000..cf1bee7a2
--- /dev/null
+++ b/tests/pipeline/star_salmon/main.nf.test
@@ -0,0 +1,187 @@
+nextflow_pipeline {
+
+    name "STAR Salmon"
+    script "main.nf"
+
+    test("with skip_qc workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                skip_qc = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 130
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with skim_trimming workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                skim_trimming = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 197
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with gtf false workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                gtf = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 198
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with star_index false workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                star_index = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 197
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with transcript_fasta false workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                transcript_fasta = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 199
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with min_mapped_reads 90 workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                min_mapped_reads = 152
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 186
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with with_umi workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                with_umi = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // FIXME ValueError: Must supply --bc-pattern for single-end
+            assert workflow.failed
+            // assert workflow.trace.tasks().size() == 186
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with with_umi skip_trimming workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                with_umi = true
+                skip_trimming = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // FIXME ValueError: Must supply --bc-pattern for single-end
+            assert workflow.failed
+            assert workflow.trace.tasks().size() == 186
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with remove_ribo_rna and skip_qualimap workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                remove_ribo_rna = true
+                skip_qualimap = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 197
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with save_align_intermeds save_reference workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                save_align_intermeds = true
+                save_reference = true
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 197
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+    test("with featurecounts_group_type false workflow parameters") {
+        when {
+            params {
+                aligner = "star_salmon"
+                featurecounts_group_type = false
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.tasks().size() == 187
+            // FIXME assert snapshot(workflow).match()
+        }
+    }
+
+}
diff --git a/tests/subworkflows/input_check/main.nf.test b/tests/subworkflows/input_check/main.nf.test
new file mode 100644
index 000000000..d468baa2c
--- /dev/null
+++ b/tests/subworkflows/input_check/main.nf.test
@@ -0,0 +1,21 @@
+nextflow_workflow {
+
+    name "input_check subworkflow"
+    script "subworkflows/local/input_check.nf"
+    workflow "INPUT_CHECK"
+
+    test("Should run without failure") {
+        when {
+            workflow {
+                """
+                input[0] = file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+    }
+
+}
diff --git a/tests/subworkflows/quantify_rsem/main.nf.test b/tests/subworkflows/quantify_rsem/main.nf.test
new file mode 100644
index 000000000..c8005aeef
--- /dev/null
+++ b/tests/subworkflows/quantify_rsem/main.nf.test
@@ -0,0 +1,25 @@
+nextflow_workflow {
+
+    name "Test quantify_rsem subworkflow"
+    script "subworkflows/local/quantify_rsem.nf"
+    workflow "QUANTIFY_RSEM"
+
+    test("Basic test") {
+        when {
+            workflow {
+                """
+                input[0] = [ [ id:'test', single_end:true ],
+                        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true)]
+
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            // FIXME
+            assert workflow.failed
+        }
+    }
+
+}
diff --git a/tests/subworkflows/quantify_salmon/main.nf.test b/tests/subworkflows/quantify_salmon/main.nf.test
new file mode 100644
index 000000000..7791e826b
--- /dev/null
+++ b/tests/subworkflows/quantify_salmon/main.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+    name "Test quantify_salmon subworkflow"
+    script "subworkflows/local/quantify_salmon.nf"
+    workflow "QUANTIFY_SALMON"
+
+    test("Basic test") {
+        when {
+            workflow {
+                """
+                input[0] = [ [ id:'test', single_end: false ],
+                            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+                            ]
+                input[1] = file(params.test_data['homo_sapiens']['genome']['index_salmon'], checkIfExists: true)
+                input[2] = file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+                input[3] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+                input[4] = true
+                input[5] = ''
+                """
+            }
+        }
+
+        then {
+            // FIXME salmon index doesn't exist
+            assert workflow.failed
+        }
+    }
+
+}
diff --git a/tests/subworkflows/quantify_salmon/test.yml b/tests/subworkflows/quantify_salmon/test.yml
new file mode 100644
index 000000000..d1d487839
--- /dev/null
+++ b/tests/subworkflows/quantify_salmon/test.yml
@@ -0,0 +1,7 @@
+- name: subworkflow quantify_salmon
+  command: nextflow run ./tests/subworkflows/local/quantify_salmon/ -entry test_quantify_salmon -c tests/config/nextflow.config
+  tags:
+    - quantify_salmon
+    - failing
+  exit_code: 1
+  # TODO files: