diff --git a/.github/include.yaml b/.github/include.yaml
new file mode 100644
index 00000000..a3629f4c
--- /dev/null
+++ b/.github/include.yaml
@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3afa7887..7df8df1f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -10,6 +10,10 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NFT_VER: "0.8.4"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -115,3 +119,116 @@ jobs:
       - name: Run pipeline with ${{ matrix.profile }} test profile
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --binqc_tool checkm --checkm_db databases/checkm
+
+  # Adam and Carson's method for running only necessary nf-tests
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      nf_test_files: ${{ steps.list.outputs.components }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.3
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
+
+      - name: print list of nf-test files
+        run: |
+          echo ${{ steps.list.outputs.components }}
+
+  nf-test:
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    needs: [changes]
+    if: needs.changes.outputs.nf_test_files != '[]'
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER:
+          - "latest-everything"
+          - "23.04"
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
+        profile:
+          - "docker"
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: |
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs:
+      - changes
+      - nf-test
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.gitignore b/.gitignore
index 5124c9ac..2eef655b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test*
diff --git a/bin/combine_tables.py b/bin/combine_tables.py
index a2dcf986..1b90b006 100755
--- a/bin/combine_tables.py
+++ b/bin/combine_tables.py
@@ -188,6 +188,7 @@ def main(args=None):
             how="outer",
         )
 
+    results.sort_values("bin", inplace=True)
     results.to_csv(args.out, sep="\t")
 
 
diff --git a/bin/get_mag_depths_summary.py b/bin/get_mag_depths_summary.py
index 69433371..7bff8189 100755
--- a/bin/get_mag_depths_summary.py
+++ b/bin/get_mag_depths_summary.py
@@ -37,6 +37,7 @@ def main(args=None):
         assembly_results = pd.read_csv(assembly_depths_file, index_col="bin", sep="\t")
         results = results.append(assembly_results, sort=True, verify_integrity=True)
 
+    results.sort_values('bin', inplace=True)
     results.to_csv(args.out, sep="\t")
 
 
diff --git a/bin/summary_busco.py b/bin/summary_busco.py
index 9701783b..c96f4150 100755
--- a/bin/summary_busco.py
+++ b/bin/summary_busco.py
@@ -219,6 +219,7 @@ def main(args=None):
     else:
         df_final = df_specific.append(df_failed)
 
+    df_final.sort_values(by="GenomeBin", inplace=True)
     df_final.to_csv(args.out, sep="\t", index=False)
 
 
diff --git a/conf/test.config b/conf/test.config
index c7a3ff3f..9ede0c1a 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -15,15 +15,17 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
+    max_cpus   = 4
+    max_memory = '15.GB'
     max_time   = '6.h'
 
     // Input data
     input                         = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.multirun.csv'
+
     centrifuge_db                 = params.pipelines_testdata_base_path + 'mag/test_data/minigut_cf.tar.gz'
     kraken2_db                    = params.pipelines_testdata_base_path + 'mag/test_data/minigut_kraken.tgz'
     skip_krona                    = false
+    megahit_fix_cpu_1             = true
     min_length_unbinned_contigs   = 1
     max_unbinned_contigs          = 2
     busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
diff --git a/conf/test_nothing.config b/conf/test_nothing.config
index e5905a9a..ceaff991 100644
--- a/conf/test_nothing.config
+++ b/conf/test_nothing.config
@@ -16,8 +16,8 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
+    max_cpus   = 4
+    max_memory = '12.GB'
     max_time   = '6.h'
 
     // Input data
diff --git a/nf-core-hyak.config b/nf-core-hyak.config
new file mode 100755
index 00000000..81c9a547
--- /dev/null
+++ b/nf-core-hyak.config
@@ -0,0 +1,34 @@
+params {
+    config_profile_description = 'UW Hyak Pedslabs cluster profile provided by nf-core/configs.'
+    config_profile_contact = 'Carson J. Miller (@CarsonJM)'
+    config_profile_url = 'https://www.peds.uw.edu/'
+    max_memory = 742.GB
+    max_cpus = 40
+    max_time = 72.h
+    }
+
+process {
+    executor = 'slurm'
+    clusterOptions = { task.attempt < 4 ? ( task.attempt < 3 ? "-A stf" : "-A stf" ) : "-A pedslabs" }
+
+    withName:'.*' {
+        queue = { task.attempt < 4 ? ( task.attempt < 3 ? 'ckpt' : 'cpu-g2-mem2x' ) : 'compute-hugemem' }
+        errorStrategy = { task.attempt < 5 ? 'retry' : 'ignore' }
+        maxRetries = 5
+        maxErrors = '-1'
+    }
+}
+
+executor {
+    queuesize = 50
+    submitRateLimit = '1 sec'
+}
+
+singularity {
+    enabled = true
+    autoMounts = true
+}
+
+debug {
+    cleanup = false
+}
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..6f5e2c47
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,10 @@
+config {
+    // Location of nf-tests
+    testsDir "."
+
+    // nf-test directory used to create temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // Location of an optional nextflow.config file specific for executing pipeline tests
+    configFile "tests/nextflow.config"
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..478cf7d1
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,64 @@
+params {
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+
+    // Base directory for nf-core/fetchngs test data
+    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
+
+    max_cpus    = 4
+    max_memory  = '12.GB'
+    time        = '2.h'
+}
+
+// Impose sensible resource limits for testing
+process {
+    withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
+        cpus   = 1
+        memory = 12.GB
+        time   = 2.h
+    }
+
+    withName: CENTRIFUGE_CENTRIFUGE {
+        cpus   = 1
+        memory = 12.GB
+        time   = 2.h
+    }
+
+    withName: BOWTIE2_ASSEMBLY_ALIGN {
+        cpus   = 1
+        memory = 12.GB
+        time   = 2.h
+    }
+
+    withName: METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
+        cpus   = 1
+        memory = 12.GB
+        time   = 2.h
+    }
+
+    withName: QUAST_BINS {
+        cpus   = 1
+        memory = 12.GB
+        time   = 2.h
+    }
+
+    withName: METABAT2_METABAT2 {
+        cpus   = 1
+        memory = 12.GB
+        time   = 2.h
+    }
+}
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = true }
+dag      { enabled = false }
+
+// Load modules test_data.config
+includeConfig 'https://github.com/nf-core/modules/raw/master/tests/config/test_data.config'
diff --git a/tests/test.nf.test b/tests/test.nf.test
new file mode 100644
index 00000000..44d0bae9
--- /dev/null
+++ b/tests/test.nf.test
@@ -0,0 +1,56 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    profile "test"
+
+    test("Profile: test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+
+
+        then {
+            def output_files = []
+            new File("$outputDir").eachFileRecurse { file -> output_files << file }
+
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    output_files.findAll {
+                        // fastp *.json
+                        // bowtie2 *.log
+                        it.toString() ==~ /.*QC_shortreads.*(json|log)/ ||
+                        // Centrifuge *kreport.txt, *report.txt, *results.txt
+                        // kraken2 *report.txt
+                        it.toString() ==~ /.*Taxonomy.*txt/ ||
+                        // MEGAHIT *.contigs.fa.gz
+                        // metaSPAdes *contigs.fasta.gz, *scaffolds.fasta.gz
+                        it.toString() ==~ /.*Assembly.*(fa\.gz|fasta\.gz)/ ||
+                        // cannot add QUAST outputs because no sample-specific prefix for report files
+                        // bowtie2 *.log
+                        it.toString() ==~ /.*Assembly.*QC.*bowtie2\.log/ ||
+                        // Prodigal *.gff.gz, *.faa.gz, *.fna.gz, *all.txt.gz
+                        // Prokka *.gff, *.err, *.faa, *.ffn, *.fna, *.fsa, *.gbk, *.tbl, *.tsv, *.txt
+                        it.toString() ==~ /.*Annotation.*(\.gz|err|faa|ffn|fna|fsa|gff|tbl|tsv|txt)/ ||
+                        // MaxBin2 *.fa.gz
+                        // MetaBAT2 *.fa.gz
+                        it.toString() ==~ /.*GenomeBinning.*fa\.gz/ ||
+                        // *depth.txt.gz
+                        it.toString() ==~ /.*GenomeBinning.*depths.*txt\.gz/ ||
+                        // bin_depths_summary.tsv, busco_summary.tsv, bin_summary.tsv
+                        it.toString() ==~ /.*GenomeBinning.*busco_summary\.tsv/
+                        // QUAST files have dates
+                    }
+                    ).match()
+                },
+                { assert new File("${outputDir}/GenomeBinning/depths/bins/bin_depths_summary.tsv").exists() },
+                { assert new File("${outputDir}/GenomeBinning/bin_summary.tsv").exists() },
+            )
+        }
+    }
+}
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
new file mode 100644
index 00000000..538189e0
--- /dev/null
+++ b/tests/test.nf.test.snap
@@ -0,0 +1,276 @@
+{
+    "Profile: test": {
+        "content": [
+            [
+                "SPAdes-MaxBin2-test_minigut_sample2.001.fa.gz:md5,6cf656f3cefd3cc7b751b707c33342fb",
+                "SPAdes-MaxBin2-test_minigut.002.fa.gz:md5,d39c16958a0c037e7b7b1d2ccd419a32",
+                "MEGAHIT-MaxBin2-test_minigut.002.fa.gz:md5,27645926966b807e9ffad8ed16c3d976",
+                "SPAdes-MaxBin2-test_minigut.001.fa.gz:md5,ddfc2eb6ca8f2a837a05a575af24a4c9",
+                "MEGAHIT-MaxBin2-test_minigut.001.fa.gz:md5,9c8ee883b97aaeccb796dd75fbe7e437",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.fa.gz:md5,edc0761106f2ab241c9b7937edcf0e43",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.fa.gz:md5,875b49fa8fa5cd5c24b5383717f1fd78",
+                "MEGAHIT-MaxBin2-test_minigut.noclass.pooled.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "MEGAHIT-MaxBin2-test_minigut.noclass.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SPAdes-MaxBin2-test_minigut.noclass.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.pooled.fa.gz:md5,361dc1b3ae1a1c4548bb4376aad3f7e2",
+                "SPAdes-MaxBin2-test_minigut.noclass.pooled.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "busco_summary.tsv:md5,ea474123f71e29463e00b4123fb8d06d",
+                "SPAdes-test_minigut_sample2-depth.txt.gz:md5,cae8059f5a82ef68a987cd9f1e1a54df",
+                "SPAdes-test_minigut-depth.txt.gz:md5,e0a777e6f79ca4ef7e05a6f4b6dfb525",
+                "MEGAHIT-test_minigut_sample2-depth.txt.gz:md5,2433c44fb396cc8e9cfbffbd4f6e9ac9",
+                "MEGAHIT-test_minigut-depth.txt.gz:md5,8cc967273e3f7d8a6d80258d790ec2f2",
+                "MEGAHIT-MetaBAT2-test_minigut.tooShort.fa.gz:md5,80cee6a312869458696444f874a54412",
+                "SPAdes-MetaBAT2-test_minigut.tooShort.fa.gz:md5,98b6d8ba42cf3a0537425155883c6cd5",
+                "SPAdes-MetaBAT2-test_minigut_sample2.tooShort.fa.gz:md5,33ba0b842d8611d8ca3b3a59c99a0f4c",
+                "MEGAHIT-MetaBAT2-test_minigut.lowDepth.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.tooShort.fa.gz:md5,ae27e657de20409403878a885cee5088",
+                "SPAdes-MetaBAT2-test_minigut_sample2.lowDepth.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SPAdes-MetaBAT2-test_minigut.lowDepth.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.lowDepth.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "MEGAHIT-MetaBAT2-test_minigut.2.fa.gz:md5,1aeab1abd23c18779cadac00a1735201",
+                "SPAdes-MetaBAT2-test_minigut.1.fa.gz:md5,80a2fd83e2e847289ca6d0f897a681e2",
+                "MEGAHIT-MetaBAT2-test_minigut.1.fa.gz:md5,90f360df42a9b977445eca1db3afc983",
+                "SPAdes-MetaBAT2-test_minigut.2.fa.gz:md5,2edd15062a0eff2424aabc6696748ab5",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.fa.gz:md5,5eeab7608c9c6db19090dc9e5d9a588c",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.fa.gz:md5,050e05a2ddb5eccc31d2116dd8b455a8",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.fa.gz:md5,841d7a48a793d278fa6125230640571b",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.fa.gz:md5,7db17fa5b89817913177db20545aa923",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.fa.gz:md5,f0817f0772a1d04601474d3ada861aa9",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fa.gz:md5,645fd3da7d9928def0c37863bbb5941c",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.2.fa.gz:md5,8d8cf802dcf4cf2b7f7ef60b48e9d17e",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.pooled.fa.gz:md5,ca6484eec7eaf321787a47173532bd6b",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.pooled.fa.gz:md5,36c8d4c273c730fa9210b65305e67224",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.pooled.fa.gz:md5,047e394c48a2affb663858093f2321c0",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.remaining.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.pooled.fa.gz:md5,e34046d231df1492056b8a461acf23e7",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.fa.gz:md5,d5c554907d9b3e549651cdbafe37d679",
+                "test_minigut_run1_phix_removed.bowtie2.log:md5,7f8750bca9c172f14c13703bfaa9aaa5",
+                "test_minigut_sample2_run0_phix_removed.bowtie2.log:md5,fb967944891311058a2c8f2255cfe118",
+                "test_minigut_run2_phix_removed.bowtie2.log:md5,7f8750bca9c172f14c13703bfaa9aaa5",
+                "test_minigut_run2_fastp.fastp.json:md5,7fdddd4a85003e38b3155b9c0a5002ae",
+                "test_minigut_run1_fastp.fastp.json:md5,ab1f5944fc9e1bd8cf51f6515b64abb3",
+                "test_minigut_sample2_run0_fastp.fastp.json:md5,2bdad74a9cc2b9727f52a83ca87e835c",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.ffn:md5,7d85b061c14f8810f8b9cfba088d43fc",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.fna:md5,050e05a2ddb5eccc31d2116dd8b455a8",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.faa:md5,2c1458a2a2563dd31f63ab457a1a746a",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.err:md5,208ed5b8e0773a1119dd88b649cd36f2",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.txt:md5,79677db5a0fb0d4b8f7a90103a894618",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.tsv:md5,16e464715c9731dff4aada01803e5aea",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.tbl:md5,2c84bb648baedaa465b58088aec5dc6b",
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+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.txt:md5,30bbcc3d0e3cb967be968eb52eb8d4eb",
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+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.gff:md5,d648b22528c2de5be07d280b5cc497eb",
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+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.txt:md5,2c38f7066e794d99fda25ecb0efcab2c",
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+                "SPAdes-MaxBin2-test_minigut_sample2.001.err:md5,f786b72ec813add37b3a0288b1546188",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.tsv:md5,1391177cbb36c47ffd24ff9e7732acd9",
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+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.err:md5,d929c37ceb764f9fc2dc75a53c1261fe",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.gff:md5,6b9e4dbae89849d84cb90683fa203be1",
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+                "SPAdes-MetaBAT2-test_minigut.2.txt:md5,2db6931e97255eeb1ae8751c316782e1",
+                "MEGAHIT-MetaBAT2-test_minigut.1.gff:md5,e87712db513239b61f4121abb1595caa",
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+                "MEGAHIT-MaxBin2-test_minigut.002.fna:md5,0c7613ea52fa34edac9d2ed9dbf2d6a5",
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+                "MEGAHIT-MaxBin2-test_minigut.002.err:md5,c0683ff54d7f72d829d32fda94afe39b",
+                "MEGAHIT-MaxBin2-test_minigut.002.txt:md5,d8a5ded06fa09215016437c90b14fb2f",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.tsv:md5,4a4b1df3d854fc5583cea95804e6efbf",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.ffn:md5,fb48ce3554f621a3d4201c3a8c23e878",
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+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.fsa:md5,91cea9abbc0fdc275ad2bf9a34273b11",
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+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.err:md5,e0726bb5d4b866929f391d7fa848d7c3",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.fna:md5,5eeab7608c9c6db19090dc9e5d9a588c",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.err:md5,cd76ba2196cfb531b19f0259470141e6",
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+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.tsv:md5,35dc68fa95bd86f874b535a1ed91ece7",
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+                "MEGAHIT-MaxBin2-test_minigut.001.txt:md5,9614328b5c70f8d371cd38cdca773c04",
+                "MEGAHIT-MaxBin2-test_minigut.001.ffn:md5,dd77303fa935c9c3424d5ea1dbbd8543",
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+                "MEGAHIT-MaxBin2-test_minigut.001.err:md5,fa8303b1e26903ec8e52e1bff79dd21b",
+                "MEGAHIT-MaxBin2-test_minigut.001.fna:md5,6220c672d932ac60c0610ebcbd7e410c",
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+                "MEGAHIT-MaxBin2-test_minigut.001.tsv:md5,bbba6ed3bfddf172a1985791c7c4be28",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.fna:md5,841d7a48a793d278fa6125230640571b",
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+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.tsv:md5,d0b4f775b834c0b8a10e9e92046de461",
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+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.txt:md5,53e804866b0120d1cf00dc76a5ca58eb",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fsa:md5,db12bdc59476dc405f0a7c0c45646b73",
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+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.tbl:md5,8e431807e39fbd7ac7b2626ecad39380",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.err:md5,9ba2b976ef27e6d053fcfa7550795a1d",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.txt:md5,fe9d30c1c4dc24c9211903a5cfcf607a",
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+                "MEGAHIT-MetaBAT2-test_minigut.2.ffn:md5,777fb719fcec732424d50772c0504462",
+                "MEGAHIT-MetaBAT2-test_minigut.2.fsa:md5,d6275158c4f23b39992e21e16d41930e",
+                "MEGAHIT-MetaBAT2-test_minigut.2.tsv:md5,8dddfab0e74cf77f0e208ad7cfe25b71",
+                "MEGAHIT-MetaBAT2-test_minigut.2.err:md5,af29244ca556b67acacb1d2f1f1ef0b7",
+                "MEGAHIT-MetaBAT2-test_minigut.2.fna:md5,1aeab1abd23c18779cadac00a1735201",
+                "MEGAHIT-MetaBAT2-test_minigut.2.faa:md5,b3c4338146bcc7fb36a8c94d92922f5e",
+                "MEGAHIT-MetaBAT2-test_minigut.2.txt:md5,3099869ba6c96cc6e61183f53d0f6e75",
+                "test_minigut_all.txt.gz:md5,8eef49811be537158db15a7dd7f50b10",
+                "test_minigut.faa.gz:md5,ddd0941359f95d2f84aabf1e5cf67557",
+                "test_minigut.fna.gz:md5,623117b4b070eeda4b6e09ece4e32e9c",
+                "test_minigut.gff.gz:md5,80e8726ecc2d146187cfa2aa4a748d84",
+                "test_minigut_sample2.gff.gz:md5,8c48d18d6234727f5490e9e23f10f468",
+                "test_minigut_sample2_all.txt.gz:md5,9f84892e7627f7f7d62945715178d803",
+                "test_minigut_sample2.fna.gz:md5,d2d62f3570d56f9bce447c07bd67e126",
+                "test_minigut_sample2.faa.gz:md5,2eab1ab73b091d2927e9f4d837c469bb",
+                "test_minigut_all.txt.gz:md5,670fd4cb6edbf454ea2b687f8bb262e4",
+                "test_minigut.faa.gz:md5,ea14477a9bafda3ad0fd61ea2e7ac62c",
+                "test_minigut.fna.gz:md5,74a15b3394053c45de3e7cd4cc27aafd",
+                "test_minigut.gff.gz:md5,d90d8730f41d31fdecf7571555b598fe",
+                "test_minigut_sample2.gff.gz:md5,3ee13f148386668e88c18a4cd6a14ad3",
+                "test_minigut_sample2_all.txt.gz:md5,b671f61078205c046b5e6ec714cfab3b",
+                "test_minigut_sample2.fna.gz:md5,aa75a86b9e67dac162e6d47301b22ee3",
+                "test_minigut_sample2.faa.gz:md5,d48a526149786c4679d21243b77df56d",
+                "SPAdes-test_minigut_sample2_contigs.fasta.gz:md5,d8c370a9f0f82bdeb55c0323702ebfa2",
+                "SPAdes-test_minigut_sample2_graph.gfa.gz:md5,2bfc49e7d40256e552ab7f4571afe424",
+                "SPAdes-test_minigut-test_minigut_sample2.bowtie2.log:md5,d8fe4dc3f2e5bb1cbc412923eed361b2",
+                "SPAdes-test_minigut.bowtie2.log:md5,53ff89dd4b11e2ad481afab3449d862e",
+                "SPAdes-test_minigut_sample2-test_minigut.bowtie2.log:md5,8160c10e3148a36b0f9647851c8427fe",
+                "SPAdes-test_minigut_sample2.bowtie2.log:md5,ab8b1e1085f54768ae564fb09b16fbe3",
+                "SPAdes-test_minigut_scaffolds.fasta.gz:md5,8bd449b393a7d3937ff74a24ce39cfc1",
+                "SPAdes-test_minigut_graph.gfa.gz:md5,15869409295ffcd300db3e99e240f252",
+                "SPAdes-test_minigut_contigs.fasta.gz:md5,7bfdf7cd015954dadde9578d59903e41",
+                "SPAdes-test_minigut_sample2_scaffolds.fasta.gz:md5,30619f032529592fbe4bd9eab5065640",
+                "MEGAHIT-test_minigut-test_minigut_sample2.bowtie2.log:md5,b9bb2fb7280f216a707f5fb3cd6b489d",
+                "MEGAHIT-test_minigut.bowtie2.log:md5,522f905d888274cc886310a1f73dfbc5",
+                "MEGAHIT-test_minigut_sample2-test_minigut.bowtie2.log:md5,7b0db12a165fdd82f4abcb5b88aa7741",
+                "MEGAHIT-test_minigut_sample2.bowtie2.log:md5,0785d7bbb739a31b736b87587ac98dc1",
+                "MEGAHIT-test_minigut_sample2.contigs.fa.gz:md5,2c0b7977b39fb2db31ee9b3adf75f8c6",
+                "MEGAHIT-test_minigut.contigs.fa.gz:md5,f35393cdbcb64bdc7ae9db78a5601229",
+                "test_minigut.kraken2_report.txt:md5,3229af9b2fcb8456ee23906f4b4a4b45",
+                "test_minigut_sample2.kraken2_report.txt:md5,7f1389d42648d2dfb423bc5fd511b730",
+                "test_minigut.results.txt:md5,36479608b6a844a8697a5f3e8416f296",
+                "test_minigut.report.txt:md5,0d038ed45d52951652cc40bce5f22e3d",
+                "test_minigut_kreport.txt:md5,558a299058d8c78b5989a4ac6168ebf7",
+                "test_minigut_sample2_kreport.txt:md5,c0c06a25e14ddb53ac67b90245d0cb83",
+                "test_minigut_sample2.results.txt:md5,9afd6683290119cd12e4c3e147c2e5a0",
+                "test_minigut_sample2.report.txt:md5,0d038ed45d52951652cc40bce5f22e3d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-07-23T11:52:04.272864191"
+    }
+}
\ No newline at end of file
diff --git a/tests/test_nothing.nf.test b/tests/test_nothing.nf.test
new file mode 100644
index 00000000..00fe98f7
--- /dev/null
+++ b/tests/test_nothing.nf.test
@@ -0,0 +1,29 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    profile "test_nothing"
+
+    test("Profile: test_nothing") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    file("$outputDir/multiqc/multiqc_data/").list().sort(),
+                    file("$outputDir/multiqc/multiqc_plots/").list().sort(),
+                    file("$outputDir/QC_shortreads/fastqc/").list().sort(),
+                    path("$outputDir/QC_shortreads/remove_phix/")
+                ).match() },
+                { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() }
+            )
+        }
+    }
+}
diff --git a/tests/test_nothing.nf.test.snap b/tests/test_nothing.nf.test.snap
new file mode 100644
index 00000000..afbf5b30
--- /dev/null
+++ b/tests/test_nothing.nf.test.snap
@@ -0,0 +1,39 @@
+{
+    "Profile: test_nothing": {
+        "content": [
+            [
+                "multiqc.log",
+                "multiqc_bowtie2.yaml",
+                "multiqc_citations.yaml",
+                "multiqc_data.json",
+                "multiqc_fastqc.yaml",
+                "multiqc_fastqc_1.yaml",
+                "multiqc_general_stats.yaml",
+                "multiqc_software_versions.yaml",
+                "multiqc_sources.yaml"
+            ],
+            [
+
+            ],
+            [
+                "test_minigut_run0_raw_1_fastqc.html",
+                "test_minigut_run0_raw_2_fastqc.html",
+                "test_minigut_run0_trimmed_1_fastqc.html",
+                "test_minigut_run0_trimmed_2_fastqc.html",
+                "test_minigut_sample2_run0_raw_1_fastqc.html",
+                "test_minigut_sample2_run0_raw_2_fastqc.html",
+                "test_minigut_sample2_run0_trimmed_1_fastqc.html",
+                "test_minigut_sample2_run0_trimmed_2_fastqc.html"
+            ],
+            [
+                "test_minigut_run0_phix_removed.bowtie2.log:md5,4f10d4bc2b3f0be722807bbf16659621",
+                "test_minigut_sample2_run0_phix_removed.bowtie2.log:md5,f1530d72fd5626bb98c60400b294dc18"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-23T14:59:09.216485918"
+    }
+}
diff --git a/workflows/mag.nf b/workflows/mag.nf
index f71d4218..36eac88d 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -881,7 +881,7 @@ workflow MAG {
                     meta, summary ->
                     ["${meta.id}.tsv", summary]
             }
-            QUAST_BINS_SUMMARY ( ch_quast_bin_summary.collect() )
+            QUAST_BINS_SUMMARY ( ch_quast_bin_summary.collect(sort:true) )
             ch_quast_bins_summary = QUAST_BINS_SUMMARY.out.summary
         }