From 7bf7d14184059d91ab8dfd1c5a7199ea5e2c9cd6 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Wed, 23 Aug 2023 15:10:38 +0200
Subject: [PATCH 1/9] Make it possible to skip multiqc with `--skip_tools`

---
 workflows/demultiplex.nf | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf
index e745588e..57dee501 100644
--- a/workflows/demultiplex.nf
+++ b/workflows/demultiplex.nf
@@ -229,24 +229,26 @@ workflow DEMULTIPLEX {
     )
 
     // MODULE: MultiQC
-    workflow_summary    = WorkflowDemultiplex.paramsSummaryMultiqc(workflow, summary_params)
-    ch_workflow_summary = Channel.value(workflow_summary)
-
-    methods_description    = WorkflowDemultiplex.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
-    ch_methods_description = Channel.value(methods_description)
-
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-    ch_multiqc_files.collect().dump(tag: "DEMULTIPLEX::MultiQC files",{FormattingService.prettyFormat(it)})
-
-    MULTIQC (
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
-    )
-    multiqc_report = MULTIQC.out.report.toList()
+    if (!("multiqc" in skip_tools)){
+        workflow_summary    = WorkflowDemultiplex.paramsSummaryMultiqc(workflow, summary_params)
+        ch_workflow_summary = Channel.value(workflow_summary)
+
+        methods_description    = WorkflowDemultiplex.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
+        ch_methods_description = Channel.value(methods_description)
+
+        ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
+        ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+        ch_multiqc_files.collect().dump(tag: "DEMULTIPLEX::MultiQC files",{FormattingService.prettyFormat(it)})
+
+        MULTIQC (
+            ch_multiqc_files.collect(),
+            ch_multiqc_config.toList(),
+            ch_multiqc_custom_config.toList(),
+            ch_multiqc_logo.toList()
+        )
+        multiqc_report = MULTIQC.out.report.toList()
+    }
 }
 
 /*

From 4df539f21ae08bc509ef155f1496bf4d1ac40ece Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:10:05 +0200
Subject: [PATCH 2/9] Check multiqc report exists in other tests

---
 tests/pipeline/skip_tools.nf.test | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test
index 1d64ddca..d336ca17 100644
--- a/tests/pipeline/skip_tools.nf.test
+++ b/tests/pipeline/skip_tools.nf.test
@@ -27,6 +27,7 @@ nextflow_pipeline {
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
+                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_trimming") }
             )
         }
@@ -54,6 +55,7 @@ nextflow_pipeline {
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
+                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_fastp") }
             )
         }
@@ -82,6 +84,7 @@ nextflow_pipeline {
                         // path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
+                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_fastqc") }
             )
         }
@@ -109,6 +112,7 @@ nextflow_pipeline {
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
+                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_fastp_fastqc") }
             )
         }

From 9c927711ad1d9715ec80da583096404a07d5bb34 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:10:20 +0200
Subject: [PATCH 3/9] Fix old test

As seen in `workflows/demultiplex.nf`, when neither trimming nor fastq
are skipped, md5 sums will only be generated for fastp files.
---
 tests/pipeline/skip_tools.nf.test | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test
index d336ca17..1a0d8bcf 100644
--- a/tests/pipeline/skip_tools.nf.test
+++ b/tests/pipeline/skip_tools.nf.test
@@ -80,8 +80,7 @@ nextflow_pipeline {
                 { assert workflow.trace.succeeded().size() == 6 },
                 { assert snapshot(
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
-                        // FIXME
-                        // path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
+                        path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001.fastp.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
                         path("$outputDir/multiqc/multiqc_report.html"),

From 6664f0151727edfe162f6175d8b4eabc97f14fcf Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:13:32 +0200
Subject: [PATCH 4/9] Add test to check MultiQC can be skipped

---
 tests/pipeline/skip_tools.nf.test | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test
index 1a0d8bcf..29c1f0d3 100644
--- a/tests/pipeline/skip_tools.nf.test
+++ b/tests/pipeline/skip_tools.nf.test
@@ -118,4 +118,32 @@ nextflow_pipeline {
 
     }
 
+    test("Skip MultiQC") {
+
+        when {
+            params {
+                input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv'
+                demultiplexer = 'bclconvert'
+                outdir        = "$outputDir"
+                skip_tools    = "multiqc"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_multiqc") },
+                { assert workflow.trace.succeeded().size() == 5 },
+                { assert !path("$outputDir/multiqc/multiqc_report.html").exists() },
+                { assert snapshot(
+                        path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
+                        path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001.fastp.fastq.gz.md5"),
+                        path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
+                        path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
+                    ).match("skip_multiqc") }
+            )
+        }
+
+    }
+
 }

From e4a1403b083abe8e498c093db870eda06c7f6468 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:13:50 +0200
Subject: [PATCH 5/9] Update snapshot

---
 tests/pipeline/skip_tools.nf.test.snap | 57 ++++++++++++++++++++------
 1 file changed, 45 insertions(+), 12 deletions(-)

diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap
index 75a1eef7..72ab1f3c 100644
--- a/tests/pipeline/skip_tools.nf.test.snap
+++ b/tests/pipeline/skip_tools.nf.test.snap
@@ -3,11 +3,12 @@
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "skip_fastqc": {
         "content": [
             "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1",
+            "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c",
             "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0",
             [
                 "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e",
@@ -22,15 +23,39 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ]
+            ],
+            "multiqc_report.html:md5,747d133098073afa11a7cca06d7f5ce1"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "skip_fastp": {
         "content": [
             "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1",
             "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,c547a3c03e7c60c871d78018ec5d933f",
             "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0",
+            [
+                "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e",
+                "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c",
+                "Demultiplex_Stats.csv:md5,93949a8cd96f907d83e0808c1ec2a04b",
+                "Demultiplex_Tile_Stats.csv:md5,83120160b0f22a1303fa1db31c19f6e9",
+                "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf",
+                "Index_Hopping_Counts.csv:md5,1059369e375fd8f8423c0f6c934be978",
+                "Quality_Metrics.csv:md5,6614accb1bb414fe312b17b81f5521f7",
+                "Quality_Tile_Metrics.csv:md5,cdc89fd2962bdd4a24f71e186112118a",
+                "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a",
+                "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
+                "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
+                "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
+            ],
+            "multiqc_report.html:md5,4cc2c41b459c91b9bc7461bf1841deca"
+        ],
+        "timestamp": "2023-08-24T06:06:42+0000"
+    },
+    "skip_multiqc": {
+        "content": [
+            "Sample1_S1_L001_R1_001.fastq.gz:md5,0a0341e2990b4fa1d9ad4b4c603144c1",
+            "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c",
+            "Undetermined_S0_L001_R1_001.fastq.gz:md5,febef808ae5397ea4ee7ee40e5fd39e0",
             [
                 "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e",
                 "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c",
@@ -46,7 +71,7 @@
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "skip_fastp_fastqc": {
         "content": [
@@ -66,27 +91,34 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ]
+            ],
+            "multiqc_report.html:md5,5a9a0289ac111ba967896f5a3f7a591d"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "software_versions_skip_fastqc": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "software_versions_skip_fastp_fastqc": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
+    },
+    "software_versions_skip_multiqc": {
+        "content": [
+            "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}"
+        ],
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "software_versions_skip_fastp": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     },
     "skip_trimming": {
         "content": [
@@ -106,8 +138,9 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ]
+            ],
+            "multiqc_report.html:md5,bd77fdcc1d1d02a3ac2e39ace3de554d"
         ],
-        "timestamp": "2023-06-15T00:02:11+0000"
+        "timestamp": "2023-08-24T06:06:42+0000"
     }
-}
\ No newline at end of file
+}

From 1a62427199b78a59a31ec0b8e3ceb2b1474dca94 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:15:52 +0200
Subject: [PATCH 6/9] Add description in schema for `skip_tools`

---
 nextflow_schema.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6102abc6..7ba6402a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -18,7 +18,8 @@
                 },
                 "skip_tools": {
                     "type": "string",
-                    "default": null
+                    "default": null,
+                    "description": "Comma-separated list of tools to skip (fastp,falco,multiqc)"
                 }
             }
         },

From c74d5b7284425d31df40fc9f491b7a97eab34f27 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:23:36 +0200
Subject: [PATCH 7/9] Fix error raising

---
 workflows/demultiplex.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf
index 57dee501..4883707a 100644
--- a/workflows/demultiplex.nf
+++ b/workflows/demultiplex.nf
@@ -21,7 +21,7 @@ def checkPathParamList = [
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { Nextflow.error 'Input samplesheet not specified!' }
+if (params.input) { ch_input = file(params.input) } else { error 'Input samplesheet not specified!' }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES
@@ -192,7 +192,7 @@ workflow DEMULTIPLEX {
             ch_versions = ch_versions.mix(SINGULAR_DEMULTIPLEX.out.versions)
             break
         default:
-            Nextflow.error "Unknown demultiplexer: ${demultiplexer}"
+            error "Unknown demultiplexer: ${demultiplexer}"
     }
     ch_raw_fastq.dump(tag: "DEMULTIPLEX::Demultiplexed Fastq",{FormattingService.prettyFormat(it)})
 
@@ -323,14 +323,14 @@ def extract_csv(input_csv, input_schema=null) {
                     diff in all_columns ? missing_columns.add(diff) : wrong_columns.add(diff)
                 }
                 if(missing_columns.size() > 0){
-                    Nextflow.error "[Samplesheet Error] The column(s) $missing_columns is/are not present. The header should look like: $all_columns"
+                    error "[Samplesheet Error] The column(s) $missing_columns is/are not present. The header should look like: $all_columns"
                 }
                 else {
-                    Nextflow.error "[Samplesheet Error] The column(s) $wrong_columns should not be in the header. The header should look like: $all_columns"
+                    error "[Samplesheet Error] The column(s) $wrong_columns should not be in the header. The header should look like: $all_columns"
                 }
             }
             else {
-                Nextflow.error "[Samplesheet Error] The columns $row are not in the right order. The header should look like: $all_columns"
+                error "[Samplesheet Error] The columns $row are not in the right order. The header should look like: $all_columns"
             }
 
         }
@@ -347,7 +347,7 @@ def extract_csv(input_csv, input_schema=null) {
             row[column] ?: missing_mandatory_columns.add(column)
         }
         if(missing_mandatory_columns.size > 0){
-            Nextflow.error "[Samplesheet Error] The mandatory column(s) $missing_mandatory_columns is/are empty on line $row_count"
+            error "[Samplesheet Error] The mandatory column(s) $missing_mandatory_columns is/are empty on line $row_count"
         }
 
         def output = []
@@ -357,7 +357,7 @@ def extract_csv(input_csv, input_schema=null) {
             content = row[key]
 
             if(!(content ==~ col.value['pattern']) && col.value['pattern'] != '' && content != '') {
-                Nextflow.error "[Samplesheet Error] The content of column '$key' on line $row_count does not match the pattern '${col.value['pattern']}'"
+                error "[Samplesheet Error] The content of column '$key' on line $row_count does not match the pattern '${col.value['pattern']}'"
             }
 
             if(col.value['content'] == 'path'){

From 5ba20d8eb19d0f05eba8a9733e34754f7d63f003 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 08:19:03 +0200
Subject: [PATCH 8/9] Add contribution to changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 172dbf18..bb6fcc7a 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#127](https://github.com/nf-core/demultiplex/pull/127) Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0
+- [#140](https://github.com/nf-core/demultiplex/pull/140) Make it possible to skip MultiQC, fix error raising
 
 ## `Removed`
 

From 14f0de78a9bc06d7d421ddf03724aeab5ffac51b Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 24 Aug 2023 09:57:55 +0200
Subject: [PATCH 9/9] Fix tests

---
 tests/pipeline/skip_tools.nf.test      |  8 +++---
 tests/pipeline/skip_tools.nf.test.snap | 34 ++++++++++++--------------
 2 files changed, 19 insertions(+), 23 deletions(-)

diff --git a/tests/pipeline/skip_tools.nf.test b/tests/pipeline/skip_tools.nf.test
index 29c1f0d3..0e4c23c1 100644
--- a/tests/pipeline/skip_tools.nf.test
+++ b/tests/pipeline/skip_tools.nf.test
@@ -22,12 +22,12 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_trimming") },
                 { assert workflow.trace.succeeded().size() == 6 },
+                { assert path("$outputDir/multiqc/multiqc_report.html").exists() },
                 { assert snapshot(
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
-                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_trimming") }
             )
         }
@@ -50,12 +50,12 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp") },
                 { assert workflow.trace.succeeded().size() == 5 },
+                { assert path("$outputDir/multiqc/multiqc_report.html").exists() },
                 { assert snapshot(
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
-                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_fastp") }
             )
         }
@@ -78,12 +78,12 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastqc") },
                 { assert workflow.trace.succeeded().size() == 6 },
+                { assert path("$outputDir/multiqc/multiqc_report.html").exists() },
                 { assert snapshot(
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001.fastp.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
-                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_fastqc") }
             )
         }
@@ -106,12 +106,12 @@ nextflow_pipeline {
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions_skip_fastp_fastqc") },
                 { assert workflow.trace.succeeded().size() == 5 },
+                { assert path("$outputDir/multiqc/multiqc_report.html").exists() },
                 { assert snapshot(
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
                         path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
-                        path("$outputDir/multiqc/multiqc_report.html"),
                     ).match("skip_fastp_fastqc") }
             )
         }
diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap
index 72ab1f3c..f6ce536e 100644
--- a/tests/pipeline/skip_tools.nf.test.snap
+++ b/tests/pipeline/skip_tools.nf.test.snap
@@ -3,7 +3,7 @@
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "skip_fastqc": {
         "content": [
@@ -23,10 +23,9 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ],
-            "multiqc_report.html:md5,747d133098073afa11a7cca06d7f5ce1"
+            ]
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "skip_fastp": {
         "content": [
@@ -46,10 +45,9 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ],
-            "multiqc_report.html:md5,4cc2c41b459c91b9bc7461bf1841deca"
+            ]
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "skip_multiqc": {
         "content": [
@@ -71,7 +69,7 @@
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
             ]
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "skip_fastp_fastqc": {
         "content": [
@@ -91,34 +89,33 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ],
-            "multiqc_report.html:md5,5a9a0289ac111ba967896f5a3f7a591d"
+            ]
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "software_versions_skip_fastqc": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "software_versions_skip_fastp_fastqc": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "software_versions_skip_multiqc": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "software_versions_skip_fastp": {
         "content": [
             "{BCLCONVERT={bclconvert=00.000.000.4.0.3}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}"
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     },
     "skip_trimming": {
         "content": [
@@ -138,9 +135,8 @@
                 "SampleSheet.csv:md5,2df2e405991814571c021dc8749c2a89",
                 "Top_Unknown_Barcodes.csv:md5,2e2faba761137f228e56bd3428453ccc",
                 "fastq_list.csv:md5,05bc84f51840f5754cfb8381b36f2cb0"
-            ],
-            "multiqc_report.html:md5,bd77fdcc1d1d02a3ac2e39ace3de554d"
+            ]
         ],
-        "timestamp": "2023-08-24T06:06:42+0000"
+        "timestamp": "2023-08-24T07:43:09+0000"
     }
-}
+}
\ No newline at end of file