From 447b03b81b00117a3a37445551992a4c93b08b1d Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Thu, 23 May 2024 15:08:22 +0000
Subject: [PATCH 1/8] Added test_nothing nf-test and updated CI

---
 .github/workflows/ci.yml        | 117 ++++++++++++++++++++++++++++++++
 .gitignore                      |   1 +
 conf/test_nothing.config        |   4 +-
 nf-test.config                  |  10 +++
 tests/nextflow.config           |  31 +++++++++
 tests/test_nothing.nf.test      |  29 ++++++++
 tests/test_nothing.nf.test.snap |  39 +++++++++++
 7 files changed, 229 insertions(+), 2 deletions(-)
 create mode 100644 nf-test.config
 create mode 100644 tests/nextflow.config
 create mode 100644 tests/test_nothing.nf.test
 create mode 100644 tests/test_nothing.nf.test.snap

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/conf/test_nothing.config b/conf/test_nothing.config
index e5905a9a..82aa8545 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 = '16.GB'
     max_time   = '6.h'
 
     // Input data
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..89da0a84
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,31 @@
+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
+    memory      = '16.GB'
+    time        = '2.h'
+}
+
+// Impose sensible resource limits for testing
+process {
+    withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
+        cpus   = 1
+        memory = 16.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 }
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"
+    }
+}

From 895f3b5b1be46401b9a23274fb493ba095eeb781 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Thu, 23 May 2024 15:45:07 +0000
Subject: [PATCH 2/8] Added include.yaml for CI

---
 .github/include.yaml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 .github/include.yaml

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

From dace37f4b20624f568f0691ce0ca8275cecadb68 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Thu, 23 May 2024 15:48:34 +0000
Subject: [PATCH 3/8] Load test_data and fix mem request

---
 conf/test_nothing.config | 2 +-
 tests/nextflow.config    | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/conf/test_nothing.config b/conf/test_nothing.config
index 82aa8545..ceaff991 100644
--- a/conf/test_nothing.config
+++ b/conf/test_nothing.config
@@ -17,7 +17,7 @@ params {
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 4
-    max_memory = '16.GB'
+    max_memory = '12.GB'
     max_time   = '6.h'
 
     // Input data
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 89da0a84..105986bf 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -6,7 +6,7 @@ params {
     pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
 
     max_cpus    = 4
-    memory      = '16.GB'
+    memory      = '12.GB'
     time        = '2.h'
 }
 
@@ -14,7 +14,7 @@ params {
 process {
     withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
         cpus   = 1
-        memory = 16.GB
+        memory = 12.GB
         time   = 2.h
     }
 }
@@ -29,3 +29,6 @@ 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'

From bbaf3022d84bfa533c78840ec378200c11076131 Mon Sep 17 00:00:00 2001
From: Carson J Miller <carsonjmiller@outlook.com>
Date: Thu, 23 May 2024 16:06:36 +0000
Subject: [PATCH 4/8] Fixed max_memory param

---
 tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 105986bf..39d10ef0 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -6,7 +6,7 @@ params {
     pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
 
     max_cpus    = 4
-    memory      = '12.GB'
+    max_memory  = '12.GB'
     time        = '2.h'
 }
 

From 486aaa70922159e222fc7e52078b20e782851a03 Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Tue, 9 Jul 2024 08:16:41 -0700
Subject: [PATCH 5/8] Second pass at snapshotting mag output

---
 bin/get_mag_depths_summary.py |   1 +
 conf/test.config              |   6 +-
 nf-core-hyak.config           |  34 ++
 tests/nextflow.config         |  58 +++
 tests/test.nf.test            |  55 +++
 tests/test.nf.test.snap       | 727 ++++++++++++++++++++++++++++++++++
 6 files changed, 879 insertions(+), 2 deletions(-)
 create mode 100755 nf-core-hyak.config
 create mode 100644 tests/test.nf.test
 create mode 100644 tests/test.nf.test.snap

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/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/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/tests/nextflow.config b/tests/nextflow.config
index 39d10ef0..21bc2b66 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -17,6 +17,25 @@ process {
         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
+    }
+
 }
 
 // Impose same minimum Nextflow version as the pipeline for testing
@@ -32,3 +51,42 @@ dag      { enabled = false }
 
 // Load modules test_data.config
 includeConfig 'https://github.com/nf-core/modules/raw/master/tests/config/test_data.config'
+
+
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// BELOW IS ONLY FOR CJM TESTING!!!
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+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 ? 'cpu-g2-mem2x' : '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/tests/test.nf.test b/tests/test.nf.test
new file mode 100644
index 00000000..2446f1ee
--- /dev/null
+++ b/tests/test.nf.test
@@ -0,0 +1,55 @@
+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|gbk|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, quast_summary.tsv, bin_summary.tsv
+                        it.toString() ==~ /.*GenomeBinning.*(bin|busco|quast|depths)_summary\.tsv/ ||
+                        // BUSCO files have dates
+                        it.toString() ==~ /.*GenomeBinning.*(summary\.tsv)/
+                    }
+                    ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
new file mode 100644
index 00000000..8dc48456
--- /dev/null
+++ b/tests/test.nf.test.snap
@@ -0,0 +1,727 @@
+{
+    "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",
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+                    [
+                        "contig_size_viewer.html:md5,6f5fa329e9f98c1f9573e63685ba991f"
+                    ],
+                    "metaquast.log:md5,91c59a23ca2c9af001c6bb42f5e6d00f",
+                    [
+                        "MEGAHIT-MetaBAT2-test_minigut-unbinned-2-fa.rna.gff:md5,df19e1b84ba6f691d20c72b397c88abf",
+                        "barrnap.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    "quast.log:md5,d9b022fc3e0dfd67901c17e3e884d8cc",
+                    "report.html:md5,c58ec1c936f7a197cfd74aef06c1bd1b",
+                    "report.pdf:md5,6aa080a90edd4074e3d2e32e34afd8df",
+                    "report.tex:md5,4592bf11940a31caafa0c45afac7b9ea",
+                    "report.tsv:md5,387dbadcf2d17af6d3d5713f5bd7ef07",
+                    "report.txt:md5,a63de2e9c5ff14c2c78254c8d2ea1d6f",
+                    "transposed_report.tex:md5,05422bfd7d8b7f23b3e79a80bac32cd7",
+                    "transposed_report.tsv:md5,966a1734f4b2a5889a1b94db42770633",
+                    "transposed_report.txt:md5,2b9b007d08cd98e2f5b99f1cc44c68dc"
+                ],
+                "report.tsv:md5,387dbadcf2d17af6d3d5713f5bd7ef07",
+                "MEGAHIT-MetaBAT2-test_minigut-unbinned-2-fa.rna.gff:md5,df19e1b84ba6f691d20c72b397c88abf",
+                "transposed_report.txt:md5,2b9b007d08cd98e2f5b99f1cc44c68dc",
+                "report.txt:md5,a63de2e9c5ff14c2c78254c8d2ea1d6f",
+                "transposed_report.tsv:md5,966a1734f4b2a5889a1b94db42770633",
+                [
+                    [
+                        "GC_content_plot.pdf:md5,2af40971939cd7e5df64935c1b4d620c",
+                        "Nx_plot.pdf:md5,177993671a25ed1b845cd0263a61f868",
+                        "SPAdes-MaxBin2-test_minigut_sample2-noclass-1-fa_coverage_histogram.pdf:md5,b7d930f73c4929c55c020fe4fee6d46b",
+                        "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.fa_GC_content_plot.pdf:md5,25079adca52be8f6048d94d71d79bb72",
+                        "coverage_histogram.pdf:md5,5e209f93bac42b8af3475a52697034ef",
+                        "cumulative_plot.pdf:md5,9ec1f9d7a0f7174de0ffa123880a3dfe"
+                    ],
+                    "icarus.html:md5,6a94ee9dc48ebc46c2d77c208e0d1d70",
+                    [
+                        "contig_size_viewer.html:md5,1ff7f0fcbeed2b8c8f5f5c1bc61f78ce"
+                    ],
+                    "metaquast.log:md5,d3e57b4abf0c5f1b314006e0e81c252a",
+                    [
+                        "SPAdes-MaxBin2-test_minigut_sample2-noclass-1-fa.rna.gff:md5,df19e1b84ba6f691d20c72b397c88abf",
+                        "barrnap.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    "quast.log:md5,56c387f605ce6774a33ab72d60e4e1f0",
+                    "report.html:md5,77b565e3df05bb8b78dd5db2f630e51d",
+                    "report.pdf:md5,eae59579fa1e74b6f4ffeffdc3c78775",
+                    "report.tex:md5,a7a668035aa793aaf18caf7f2248b272",
+                    "report.tsv:md5,3fe6c3d71fa0fcd029ca4aaf555674a7",
+                    "report.txt:md5,7d3b8c09cc6d954c3fd81b66a2c27a6a",
+                    "transposed_report.tex:md5,43c1f1b9d9127c7481ddd22c9410a68c",
+                    "transposed_report.tsv:md5,08640deb524b1e8b06fe7b63baaa6e09",
+                    "transposed_report.txt:md5,e5034b301f0c2a326312bd562f571839"
+                ],
+                "report.tsv:md5,3fe6c3d71fa0fcd029ca4aaf555674a7",
+                "SPAdes-MaxBin2-test_minigut_sample2-noclass-1-fa.rna.gff:md5,df19e1b84ba6f691d20c72b397c88abf",
+                "transposed_report.txt:md5,e5034b301f0c2a326312bd562f571839",
+                "report.txt:md5,7d3b8c09cc6d954c3fd81b66a2c27a6a",
+                "transposed_report.tsv:md5,08640deb524b1e8b06fe7b63baaa6e09",
+                "SPAdes-MetaBAT2-unclassified-unrefined_unbinned-test_minigut_sample2-quast_summary.tsv:md5,f0b7f75e7a24728be2776180e47bf097",
+                "SPAdes-MaxBin2-unclassified-unrefined-test_minigut-quast_summary.tsv:md5,f0455a9ab08a31621681ae505d498528",
+                [
+                    [
+                        "GC_content_plot.pdf:md5,641c1a4d957439003b60ba7da7691258",
+                        "Nx_plot.pdf:md5,a5b294cca9801d24a17b7a5bfe1a49b6",
+                        "SPAdes-MetaBAT2-test_minigut_sample2-unbinned-2-fa_coverage_histogram.pdf:md5,c4af6c1e5a1d7fe22abc044f43086043",
+                        "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.fa_GC_content_plot.pdf:md5,a9750cc07193744418374263ba1ae114",
+                        "coverage_histogram.pdf:md5,59d814925cc3b2972231aeecfa47c364",
+                        "cumulative_plot.pdf:md5,7e68174473aa29e8c6b01940d89aebb7"
+                    ],
+                    "icarus.html:md5,ac29090e6be12259575d2a1dd2173ea9",
+                    [
+                        "contig_size_viewer.html:md5,70b6ecdb928e04c6c6caa5334b903e6a"
+                    ],
+                    "metaquast.log:md5,8dbd333a59eeb87b409be36e8e9880e3",
+                    [
+                        "SPAdes-MetaBAT2-test_minigut_sample2-unbinned-2-fa.rna.gff:md5,d79108cff0a749862217742356970b9a",
+                        "barrnap.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
+                    "quast.log:md5,482d94af4799500cc85795e24998a405",
+                    "report.html:md5,d1e7c0dd3e2d2ea7dc9be4ec304ae5e9",
+                    "report.pdf:md5,b453c7616d8f8854a641ce630b8db384",
+                    "report.tex:md5,4c3a66e77f98097b95cba5f476320d89",
+                    "report.tsv:md5,e9eca4fd19c7c3fb3068922bf6078641",
+                    "report.txt:md5,09cf365e064c614c880dc697defb16e4",
+                    "transposed_report.tex:md5,ab660f32c90d54a9c8a94c77cd3c2b9e",
+                    "transposed_report.tsv:md5,a3d91194541133324287f87664fe9a80",
+                    "transposed_report.txt:md5,93d80564df7ae7cf4da34a05fa9dd839"
+                ],
+                "report.tsv:md5,e9eca4fd19c7c3fb3068922bf6078641",
+                "SPAdes-MetaBAT2-test_minigut_sample2-unbinned-2-fa.rna.gff:md5,d79108cff0a749862217742356970b9a",
+                "transposed_report.txt:md5,93d80564df7ae7cf4da34a05fa9dd839",
+                "report.txt:md5,09cf365e064c614c880dc697defb16e4",
+                "transposed_report.tsv:md5,a3d91194541133324287f87664fe9a80",
+                "MEGAHIT-MetaBAT2-unclassified-unrefined_unbinned-test_minigut-quast_summary.tsv:md5,670c1bf14ade6c373f2f9f14bb12eb2a",
+                "SPAdes-test_minigut_sample2-depth.txt.gz:md5,f102b98b95249c3084eca6a3013838de",
+                "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",
+                "bin_depths_summary.tsv:md5,ba83d029531fc295c6410083e69e52d4",
+                "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:md5,3e603ca31105651ebce03689ecde9eec",
+                "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:md5,7db17fa5b89817913177db20545aa923",
+                "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:md5,74a4e09b094ea5903cf9cea79e94ed57",
+                "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",
+                "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": "2024-06-28T14:55:58.500290094"
+    }
+}
\ No newline at end of file

From acbd6052270c450444be2b663bf423296170c8eb Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Tue, 23 Jul 2024 12:10:20 -0700
Subject: [PATCH 6/8] Sorted output TSV files to address inconsistent hashes

---
 bin/combine_tables.py   |   1 +
 bin/summary_busco.py    |   1 +
 tests/nextflow.config   |  11 +
 tests/test.nf.test      |  13 +-
 tests/test.nf.test.snap | 805 +++++++++-------------------------------
 workflows/mag.nf        |   2 +-
 6 files changed, 198 insertions(+), 635 deletions(-)

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/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/tests/nextflow.config b/tests/nextflow.config
index 21bc2b66..d2d63668 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -36,6 +36,17 @@ process {
         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
diff --git a/tests/test.nf.test b/tests/test.nf.test
index 2446f1ee..44d0bae9 100644
--- a/tests/test.nf.test
+++ b/tests/test.nf.test
@@ -36,19 +36,20 @@ nextflow_pipeline {
                         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|gbk|gff|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, quast_summary.tsv, bin_summary.tsv
-                        it.toString() ==~ /.*GenomeBinning.*(bin|busco|quast|depths)_summary\.tsv/ ||
-                        // BUSCO files have dates
-                        it.toString() ==~ /.*GenomeBinning.*(summary\.tsv)/
+                        // 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
index 8dc48456..538189e0 100644
--- a/tests/test.nf.test.snap
+++ b/tests/test.nf.test.snap
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-                "SPAdes-MaxBin2-unclassified-unrefined-test_minigut-quast_summary.tsv:md5,f0455a9ab08a31621681ae505d498528",
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-                "SPAdes-MetaBAT2-test_minigut_sample2-unbinned-2-fa.rna.gff:md5,d79108cff0a749862217742356970b9a",
-                "transposed_report.txt:md5,93d80564df7ae7cf4da34a05fa9dd839",
-                "report.txt:md5,09cf365e064c614c880dc697defb16e4",
-                "transposed_report.tsv:md5,a3d91194541133324287f87664fe9a80",
-                "MEGAHIT-MetaBAT2-unclassified-unrefined_unbinned-test_minigut-quast_summary.tsv:md5,670c1bf14ade6c373f2f9f14bb12eb2a",
-                "SPAdes-test_minigut_sample2-depth.txt.gz:md5,f102b98b95249c3084eca6a3013838de",
+                "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",
-                "bin_depths_summary.tsv:md5,ba83d029531fc295c6410083e69e52d4",
                 "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",
@@ -657,16 +35,16 @@
                 "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:md5,3e603ca31105651ebce03689ecde9eec",
+                "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:md5,7db17fa5b89817913177db20545aa923",
+                "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:md5,74a4e09b094ea5903cf9cea79e94ed57",
+                "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",
@@ -676,6 +54,177 @@
                 "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",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.fsa:md5,17768f15abd14f593c2749e68c09fb07",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.1.gff:md5,234b0fef691681ba8657ac0836d0d4b2",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.err:md5,26962705c676f650d204c18b4628949d",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.tsv:md5,be414fbd7308433ef4314a308cc322d2",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.tbl:md5,c283f6e90f412846b93084e80585f34b",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.fna:md5,edc0761106f2ab241c9b7937edcf0e43",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.gff:md5,c87208bd24ead2bc9eba43bcc1d9c131",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.txt:md5,9b35686601869ab8f5d399a75df82b87",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.fsa:md5,963052ff92178835ca9795d51b71c591",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.ffn:md5,5874ca25f5b20a6fdaf984ab4c13b690",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.2.faa:md5,9f49714e3cb2642bf41c2ca33f274722",
+                "SPAdes-MaxBin2-test_minigut.002.fsa:md5,1f5b9d09118a65d033d6d5488c77a423",
+                "SPAdes-MaxBin2-test_minigut.002.txt:md5,41510799f001ba18cea11a9ea3212b99",
+                "SPAdes-MaxBin2-test_minigut.002.tsv:md5,5ada1a4b5f2b4fa0eed0af06c2a7e9ee",
+                "SPAdes-MaxBin2-test_minigut.002.fna:md5,c69eb3a9bac20d75b492e2adb61b846e",
+                "SPAdes-MaxBin2-test_minigut.002.faa:md5,846a091d4f412975bcd66c5ef0ed49d9",
+                "SPAdes-MaxBin2-test_minigut.002.gff:md5,66d6702dde9a83282fdfa2235415da43",
+                "SPAdes-MaxBin2-test_minigut.002.tbl:md5,79c0b0d73771ae809c5ab8320be23c13",
+                "SPAdes-MaxBin2-test_minigut.002.ffn:md5,cfa06978f6c645f6d1bf317422645665",
+                "SPAdes-MaxBin2-test_minigut.002.err:md5,086a84d75ae6e025ee2a335318740639",
+                "SPAdes-MetaBAT2-test_minigut.1.ffn:md5,695be962643c21f73cdb187a20778b4b",
+                "SPAdes-MetaBAT2-test_minigut.1.gff:md5,dc8b584a3fac76a840117d04e09aed96",
+                "SPAdes-MetaBAT2-test_minigut.1.faa:md5,2879b7a33cca4024e3c518b2fa4bc063",
+                "SPAdes-MetaBAT2-test_minigut.1.err:md5,418d898f18f2d5e55d355ac3bba76dc4",
+                "SPAdes-MetaBAT2-test_minigut.1.fna:md5,80a2fd83e2e847289ca6d0f897a681e2",
+                "SPAdes-MetaBAT2-test_minigut.1.txt:md5,dd64a6fd054a787886cb1f0b72e9f60f",
+                "SPAdes-MetaBAT2-test_minigut.1.fsa:md5,2bca9c656521f70c19f43079507d7fa0",
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+                "SPAdes-MetaBAT2-test_minigut.1.tsv:md5,43cab99c30996e788ef8425a8a5a2688",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.2.err:md5,b5c20459962c51eab03362e5054f6132",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.2.tbl:md5,31b9e669fe3042f78c868adf7939a132",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.2.tsv:md5,f829c9535ae4b775e1e3d454d280e3b9",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.2.gff:md5,abb9a2a784ea6ccf0f3094f688a1bd33",
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+                "SPAdes-MetaBAT2-test_minigut.unbinned.2.fsa:md5,61d395c89c68621cb62ae5b6fda9dd75",
+                "SPAdes-MaxBin2-test_minigut.001.faa:md5,7e773008946a8eeb529cabc153d197b5",
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+                "SPAdes-MaxBin2-test_minigut.001.err:md5,e4a6a1260695dcaf7f9c77d36f1c5484",
+                "SPAdes-MaxBin2-test_minigut.001.fna:md5,61260ff67968048081cf49e873c8c778",
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+                "SPAdes-MaxBin2-test_minigut.001.tbl:md5,8edadf2a9fb87f52b69f7b51bb82743c",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.ffn:md5,4dd70eabe8c0e34afaf644b70d7b52ac",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.txt:md5,30bbcc3d0e3cb967be968eb52eb8d4eb",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.faa:md5,3e1c867524ba5db4daae5d59e470a3ad",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.fna:md5,f0817f0772a1d04601474d3ada861aa9",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.tbl:md5,a804c8f70d33fd645d8a3047bc39e799",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.tsv:md5,50ac39fdc58d4810a02ba3034472ca69",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.fsa:md5,32d91312e135d672c1897db3b94c611d",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.err:md5,581881a988afcbe4f84d279867aedda3",
+                "SPAdes-MetaBAT2-test_minigut_sample2.unbinned.2.gff:md5,d648b22528c2de5be07d280b5cc497eb",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.fna:md5,875b49fa8fa5cd5c24b5383717f1fd78",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.tsv:md5,39dbe3ff37b7d6cd5d00fdf1151fae96",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.ffn:md5,0ac53e00c8ffdb33fe198b0918212346",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.err:md5,97c5e09f898bbfe41a2a1bc80e195a26",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.txt:md5,2c38f7066e794d99fda25ecb0efcab2c",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.fsa:md5,69126c9190edcc89f2a6350add9e3a33",
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+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.tbl:md5,c23cf1ec1bf158821e69e86eb145f12c",
+                "SPAdes-MaxBin2-test_minigut_sample2.noclass.1.faa:md5,533017d471f5e50c65cc3102a923f75c",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.txt:md5,463a09b3db39d535a5316245817ed4f5",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.faa:md5,e33d7a55af8b070646de60f62d407481",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.fsa:md5,698cbda6252cc9dce4f9f4ff7022550a",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.tbl:md5,37d673f1ccc3a57dcbb0ba09d60ed99c",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.gff:md5,5ae3a120458562b90c2d8a25d02a5cca",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.err:md5,f786b72ec813add37b3a0288b1546188",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.tsv:md5,1391177cbb36c47ffd24ff9e7732acd9",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.ffn:md5,97dc6f19dde7856ffeeec82e41975eba",
+                "SPAdes-MaxBin2-test_minigut_sample2.001.fna:md5,6f1fce38dc6fc93407ad72c0332f6ea4",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.txt:md5,d880c401161aff3752a0a65f7cda1d76",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.fna:md5,7db17fa5b89817913177db20545aa923",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.ffn:md5,9b99af65a7f982bf0caa48cf311fb4a1",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.tsv:md5,30a2479050774bf9853205f425a753eb",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.faa:md5,58f5d100f8278cd9192002302e48b4d3",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.tbl:md5,640c49ea52dc20984f695fb9feac11dc",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.err:md5,d929c37ceb764f9fc2dc75a53c1261fe",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.gff:md5,6b9e4dbae89849d84cb90683fa203be1",
+                "SPAdes-MetaBAT2-test_minigut.unbinned.1.fsa:md5,e70fd97939c6ebab696458c3a4e82284",
+                "SPAdes-MetaBAT2-test_minigut.2.fna:md5,2edd15062a0eff2424aabc6696748ab5",
+                "SPAdes-MetaBAT2-test_minigut.2.fsa:md5,a86850303207873193860fc58f1ffbc0",
+                "SPAdes-MetaBAT2-test_minigut.2.gff:md5,c03234fef3b706f10414738e07717eab",
+                "SPAdes-MetaBAT2-test_minigut.2.faa:md5,1cc11d484e49ff51111b0e0bf7a2349b",
+                "SPAdes-MetaBAT2-test_minigut.2.ffn:md5,11b5110cbe5081a136bf256a98096b6c",
+                "SPAdes-MetaBAT2-test_minigut.2.err:md5,c357f1471801090171849ae77581f993",
+                "SPAdes-MetaBAT2-test_minigut.2.tbl:md5,5cf8d2cb3c446c80f4926b58964ab231",
+                "SPAdes-MetaBAT2-test_minigut.2.tsv:md5,69c5f665da89f120f820610f0f91592e",
+                "SPAdes-MetaBAT2-test_minigut.2.txt:md5,2db6931e97255eeb1ae8751c316782e1",
+                "MEGAHIT-MetaBAT2-test_minigut.1.gff:md5,e87712db513239b61f4121abb1595caa",
+                "MEGAHIT-MetaBAT2-test_minigut.1.txt:md5,d3d202bb1e979f5810b306c9eca5c4d3",
+                "MEGAHIT-MetaBAT2-test_minigut.1.err:md5,64c49c0fa3e86a5f0a4805db76873a62",
+                "MEGAHIT-MetaBAT2-test_minigut.1.ffn:md5,b15e9e416562188c7e33766765cd6589",
+                "MEGAHIT-MetaBAT2-test_minigut.1.fna:md5,90f360df42a9b977445eca1db3afc983",
+                "MEGAHIT-MetaBAT2-test_minigut.1.tbl:md5,f062d18eace5fbb1923ca5fef9ad0175",
+                "MEGAHIT-MetaBAT2-test_minigut.1.tsv:md5,ed24015a68c04266ef00d7c8b9d63cc2",
+                "MEGAHIT-MetaBAT2-test_minigut.1.faa:md5,b9bd97482ed409c39f8685a9bc898f01",
+                "MEGAHIT-MetaBAT2-test_minigut.1.fsa:md5,41f9af305bb648fada0ed8077ca17620",
+                "MEGAHIT-MaxBin2-test_minigut.002.fna:md5,0c7613ea52fa34edac9d2ed9dbf2d6a5",
+                "MEGAHIT-MaxBin2-test_minigut.002.ffn:md5,61914f39790355629a17f2c26d969cf5",
+                "MEGAHIT-MaxBin2-test_minigut.002.tsv:md5,5690bc322e7d0d454552d927a5106b88",
+                "MEGAHIT-MaxBin2-test_minigut.002.gff:md5,2f97e173c67d03ddf5a02f067a112cca",
+                "MEGAHIT-MaxBin2-test_minigut.002.fsa:md5,064528e4713d7496fbdc4f63fcf31c9c",
+                "MEGAHIT-MaxBin2-test_minigut.002.faa:md5,78099bcfdbc895f9a9db06cd15f5edab",
+                "MEGAHIT-MaxBin2-test_minigut.002.tbl:md5,cf748d9877caac9621989c88164a425a",
+                "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",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.txt:md5,30bbcc3d0e3cb967be968eb52eb8d4eb",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.fsa:md5,91cea9abbc0fdc275ad2bf9a34273b11",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.gff:md5,5000e09fb766377cbecf3c52e090b445",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.faa:md5,c477cb21cd5809cd1793de5639900f93",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.1.tbl:md5,e59dd535e34ba318224b7fddc50e6e41",
+                "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",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.tbl:md5,fdd304ae6fd459fa09f54cb2ca31e5ba",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.tsv:md5,35dc68fa95bd86f874b535a1ed91ece7",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.fna:md5,d5c554907d9b3e549651cdbafe37d679",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.fsa:md5,105497c9ccaef743fd246354ae57d56f",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.faa:md5,617e2541ac30bc3d43009fbb0b82be4b",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.txt:md5,1c279fd7b982a362402f68e3d5965747",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.ffn:md5,b2acc3e267abffd74b221a047fe0922e",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.2.gff:md5,02bbc64f305ecc93fcf56bf89b27e305",
+                "MEGAHIT-MaxBin2-test_minigut.001.txt:md5,9614328b5c70f8d371cd38cdca773c04",
+                "MEGAHIT-MaxBin2-test_minigut.001.ffn:md5,dd77303fa935c9c3424d5ea1dbbd8543",
+                "MEGAHIT-MaxBin2-test_minigut.001.gff:md5,c34edb50855659e55bb4a45797648558",
+                "MEGAHIT-MaxBin2-test_minigut.001.fsa:md5,f415709e8e654d5791b842e896e75024",
+                "MEGAHIT-MaxBin2-test_minigut.001.faa:md5,eaccd450eed58eae731384315670ca58",
+                "MEGAHIT-MaxBin2-test_minigut.001.err:md5,fa8303b1e26903ec8e52e1bff79dd21b",
+                "MEGAHIT-MaxBin2-test_minigut.001.fna:md5,6220c672d932ac60c0610ebcbd7e410c",
+                "MEGAHIT-MaxBin2-test_minigut.001.tbl:md5,27d651583f776e4be78dc3309a1489c4",
+                "MEGAHIT-MaxBin2-test_minigut.001.tsv:md5,bbba6ed3bfddf172a1985791c7c4be28",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.fna:md5,841d7a48a793d278fa6125230640571b",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.err:md5,dfa8bb02e74ee0560e615a68ab2a7511",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.tsv:md5,d0b4f775b834c0b8a10e9e92046de461",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.gff:md5,cdb3eb921bdb702c208a4c6a9205d3af",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.fsa:md5,a441911e5a5f2122ea1709dbbab2c04d",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.ffn:md5,a39966c556b21b263d50a39624bb1e65",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.faa:md5,6d54558d192c12023a56e29a5545729e",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.tbl:md5,adb6e64476013ab82efd6dbe6791e142",
+                "MEGAHIT-MetaBAT2-test_minigut_sample2.unbinned.2.txt:md5,53e804866b0120d1cf00dc76a5ca58eb",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fsa:md5,db12bdc59476dc405f0a7c0c45646b73",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.ffn:md5,70a135cd81f6eaee9cb74406b1c083b4",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.fna:md5,645fd3da7d9928def0c37863bbb5941c",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.gff:md5,046cef819141b49559e209c948128ff8",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.tsv:md5,bf6389be0ee3d0cd109272e393a58304",
+                "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",
+                "MEGAHIT-MetaBAT2-test_minigut.unbinned.1.faa:md5,bd924d3da4d0381b103a12430ca4d449",
+                "MEGAHIT-MetaBAT2-test_minigut.2.tbl:md5,88b32cb40fbfa8266eff7d8c2d6ab7c2",
+                "MEGAHIT-MetaBAT2-test_minigut.2.gff:md5,c574ead3dea6518248829e1ec51ca1bf",
+                "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",
@@ -722,6 +271,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.1"
         },
-        "timestamp": "2024-06-28T14:55:58.500290094"
+        "timestamp": "2024-07-23T11:52:04.272864191"
     }
 }
\ No newline at end of file
diff --git a/workflows/mag.nf b/workflows/mag.nf
index 7594b370..c06349f5 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
         }
 

From 9b1def76f78e3a2ed0f09ed7b37bc8bdf764695c Mon Sep 17 00:00:00 2001
From: Carson J Miller <68351153+CarsonJM@users.noreply.github.com>
Date: Tue, 23 Jul 2024 12:14:49 -0700
Subject: [PATCH 7/8] Delete tests/nextflow.config

---
 tests/nextflow.config | 103 ------------------------------------------
 1 file changed, 103 deletions(-)
 delete mode 100644 tests/nextflow.config

diff --git a/tests/nextflow.config b/tests/nextflow.config
deleted file mode 100644
index d2d63668..00000000
--- a/tests/nextflow.config
+++ /dev/null
@@ -1,103 +0,0 @@
-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'
-
-
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-// BELOW IS ONLY FOR CJM TESTING!!!
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-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 ? 'cpu-g2-mem2x' : '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
-}

From 5619352aeca70100d25191d0feccb349e1783a5d Mon Sep 17 00:00:00 2001
From: "Carson J. Miller" <carsonjmiller@outlook.com>
Date: Tue, 23 Jul 2024 12:22:04 -0700
Subject: [PATCH 8/8] Add tests/nextflow.config

---
 tests/nextflow.config | 64 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 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'