diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6fef5f23..df00beb4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
+          - "latest-stable"
         profile:
           - "docker"
           - "singularity"
@@ -102,8 +102,6 @@ jobs:
       - name: Run Tests (Shard ${{ matrix.shard }}/6)
         run: |
           nf-test test \
-              --debug \
-              --verbose \
               --ci \
               --shard ${{ matrix.shard }}/6 \
               --changed-since HEAD^ \
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 184a9c34..392f7718 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev
+## 1.5.2dev - (UNRELEASED)
+
+### `Added`
+
+### `Changed`
+
+- [#276](https://github.com/nf-core/demultiplex/pull/276) Template update for nf-core/tools v3.0.2
+
+### `Fixed`
+
+- [#277](https://github.com/nf-core/demultiplex/pull/277) Improved samplesheet generation to always produce all types of samplesheets, added the ability to explicitly set strandedness, and fixed output paths to correctly reflect the `publishDir` subdirectory structure.
 
 ## 1.5.2 - 2024-10-07
 
diff --git a/modules/local/fastq_to_samplesheet/main.nf b/modules/local/fastq_to_samplesheet/main.nf
index f79cabcf..92429d51 100644
--- a/modules/local/fastq_to_samplesheet/main.nf
+++ b/modules/local/fastq_to_samplesheet/main.nf
@@ -14,15 +14,18 @@ process FASTQ_TO_SAMPLESHEET {
 
     exec:
 
+    // Calculate the dynamic output directory based on meta.lane
+    def outputDir = meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}"
+
     // Add relevant fields to the map
     def pipeline_map = [
         sample  : meta.samplename,
-        fastq_1 : meta.fastq_1
+        fastq_1 : outputDir + '/' + file(meta.fastq_1).fileName
     ]
 
     // Add fastq_2 if it's a paired-end sample
     if (!meta.single_end) {
-        pipeline_map.fastq_2 = meta.fastq_2
+        pipeline_map.fastq_2 = outputDir + '/' + file(meta.fastq_2).fileName
     }
 
     // Add pipeline-specific entries
diff --git a/nextflow.config b/nextflow.config
index df00afee..8d9a6b81 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -27,7 +27,7 @@ params {
     kraken_db                   = null         // file .tar.gz
 
     // Downstream Nextflow pipeline
-    downstream_pipeline         = "default"     // enum string [rnaseq, atacseq, taxprofiler, default]
+    strandedness                = "auto"        // enum string [auto, reverse, forward, unstranded]
 
     // Options: CheckQC
     checkqc_config              = []            // file .yaml
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9857da5d..bddff01c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -35,12 +35,6 @@
                     "type": "string",
                     "format": "file-path",
                     "description": "Path to Illumina v2 samplesheet validator .json file"
-                },
-                "downstream_pipeline": {
-                    "type": "string",
-                    "description": "Name of downstream nf-core pipeline (one of: rnaseq, atacseq, taxprofiler or default). Used to produce the input samplesheet for that pipeline.",
-                    "default": "default",
-                    "enum": ["rnaseq", "atacseq", "taxprofiler", "default"]
                 }
             }
         },
@@ -276,5 +270,11 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ]
+    ],
+    "properties": {
+        "strandedness": {
+            "type": "string",
+            "default": "auto"
+        }
+    }
 }
diff --git a/tests/.nftignore b/tests/.nftignore
index 2c7e41e2..5b668254 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -22,7 +22,7 @@ multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
-samplesheet/samplesheet.csv
+samplesheet/*.csv
 sim-data/*-Bases2Fastq-Sim_QC.html
 sim-data/*.fastp.fastq.gz
 sim-data/*.fastp.fastq.gz.md5
diff --git a/tests/bases2fastq.nf.test.snap b/tests/bases2fastq.nf.test.snap
index 317657ae..7a8c9b96 100644
--- a/tests/bases2fastq.nf.test.snap
+++ b/tests/bases2fastq.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Bases2Fastq": {
         "content": [
-            8,
+            10,
             {
                 "BASES2FASTQ": {
                     "bases2fastq": "1.8.0.1260801529, use subject to license available at elementbiosciences.com"
@@ -23,7 +23,7 @@
                 }
             },
             [
-        "fastq",
+                "fastq",
                 "fastq/DefaultSample.samplesheet.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
@@ -148,7 +148,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv",
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv",
                 "sim-data",
                 "sim-data.csv",
                 "sim-data/20230404-Bases2Fastq-Sim_QC.html",
@@ -210,8 +212,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T16:37:55.855747"
+        "timestamp": "2024-10-17T23:29:10.785062467"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/bcl2fastq.nf.test.snap b/tests/bcl2fastq.nf.test.snap
index 7fb8ea17..cdda06ef 100644
--- a/tests/bcl2fastq.nf.test.snap
+++ b/tests/bcl2fastq.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Bcl2Fastq": {
         "content": [
-            6,
+            8,
             {
                 "BCL2FASTQ": {
                     "bcl2fastq": "2.20.0.422"
@@ -191,7 +191,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -237,8 +239,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T16:39:25.304794"
+        "timestamp": "2024-10-17T23:30:33.296858681"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/bclconvert.nf.test.snap b/tests/bclconvert.nf.test.snap
index f064c458..1339d5e3 100644
--- a/tests/bclconvert.nf.test.snap
+++ b/tests/bclconvert.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "BCL-CONVERT": {
         "content": [
-            6,
+            8,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -177,7 +177,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -233,8 +235,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T16:41:01.01928"
+        "timestamp": "2024-10-17T23:31:58.719385372"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/bclconvert_mini.nf.test.snap b/tests/bclconvert_mini.nf.test.snap
index 77ba8a65..8bdd4e5c 100644
--- a/tests/bclconvert_mini.nf.test.snap
+++ b/tests/bclconvert_mini.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "BCL-CONVERT-mini": {
         "content": [
-            26,
+            38,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -248,7 +248,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "HBRR1_S1_L001.fastp.fastq.gz:md5,451657490d4816dd5ff904e34ecc7fdf",
@@ -346,8 +348,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-16T10:59:08.175426"
+        "timestamp": "2024-10-17T23:34:50.670465424"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/fqtk.nf.test b/tests/fqtk.nf.test
index 3dea13d8..cd1841a1 100644
--- a/tests/fqtk.nf.test
+++ b/tests/fqtk.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     profile "test_fqtk"
     tag "fqtk"
+    tag "pipeline"
 
     test("FQTK") {
 
diff --git a/tests/fqtk.nf.test.snap b/tests/fqtk.nf.test.snap
index c5cbb5ec..24a3644f 100644
--- a/tests/fqtk.nf.test.snap
+++ b/tests/fqtk.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "FQTK": {
         "content": [
-            129,
+            179,
             {
                 "CSV2TSV": {
                     "sed": 4.8
@@ -169,7 +169,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv",
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv",
                 "test",
                 "test.csv",
                 "test/demux-metrics.txt",
@@ -728,8 +730,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T16:56:01.494868"
+        "timestamp": "2024-10-17T23:37:31.252912431"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/kraken.nf.test.snap b/tests/kraken.nf.test.snap
index 36a6b165..7cdd3b53 100644
--- a/tests/kraken.nf.test.snap
+++ b/tests/kraken.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "kraken2": {
         "content": [
-            9,
+            11,
             {
                 "BCL2FASTQ": {
                     "bcl2fastq": "2.20.0.422"
@@ -205,7 +205,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -255,8 +257,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T16:57:22.70902"
+        "timestamp": "2024-10-17T23:39:05.363547947"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/mkfastq.nf.test.snap b/tests/mkfastq.nf.test.snap
index c95a793e..155a792f 100644
--- a/tests/mkfastq.nf.test.snap
+++ b/tests/mkfastq.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "MKFASTQ": {
         "content": [
-            10,
+            14,
             {
                 "CELLRANGER_MKFASTQ": {
                     "cellranger": "8.0.0"
@@ -161,7 +161,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "cellranger-tiny-bcl-simple.lane1_no_adapters.csv:md5,86a945ab9d579c7bc98d43f76a07118b",
@@ -200,8 +202,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T14:34:23.682439"
+        "timestamp": "2024-10-17T23:40:20.21203835"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/sgdemux.nf.test.snap b/tests/sgdemux.nf.test.snap
index e11ba9ee..285d4c9c 100644
--- a/tests/sgdemux.nf.test.snap
+++ b/tests/sgdemux.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "SGDEMUX": {
         "content": [
-            128,
+            178,
             {
                 "FALCO": {
                     "falco": "1.2.1"
@@ -204,7 +204,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv",
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv",
                 "sim-data",
                 "sim-data.csv",
                 "sim-data/Undetermined_S25_L001.fastp.html",
@@ -580,6 +582,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T16:07:45.042862"
+        "timestamp": "2024-10-18T00:54:45.989490742"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/skip_tools.nf.test.snap b/tests/skip_tools.nf.test.snap
index a7b0d626..4a414e55 100644
--- a/tests/skip_tools.nf.test.snap
+++ b/tests/skip_tools.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Skip Fastp": {
         "content": [
-            5,
+            7,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -139,7 +139,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -186,13 +188,13 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T11:16:29.215413"
+        "timestamp": "2024-10-18T00:25:42.942384924"
     },
     "Skip Trimming": {
         "content": [
-            6,
+            8,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -367,7 +369,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -422,13 +426,13 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T14:36:31.319794"
+        "timestamp": "2024-10-18T00:24:59.739085162"
     },
     "Skip MultiQC": {
         "content": [
-            5,
+            7,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -485,7 +489,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -519,13 +525,13 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T11:20:29.598072"
+        "timestamp": "2024-10-18T00:29:21.376431772"
     },
     "Skip Fastp & Fastqc": {
         "content": [
-            5,
+            7,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -663,7 +669,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -710,13 +718,13 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T11:19:11.741332"
+        "timestamp": "2024-10-18T00:28:05.245862992"
     },
     "Skip Fastqc": {
         "content": [
-            6,
+            8,
             {
                 "BCLCONVERT": {
                     "bclconvert": "4.3.6"
@@ -892,7 +900,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv:md5,ee5db2e12754e069998b0a96e535238c",
@@ -948,8 +958,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T14:38:35.728344"
+        "timestamp": "2024-10-18T00:27:11.29098668"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/test_pe.nf.test.snap b/tests/test_pe.nf.test.snap
index 4e4248e6..eaebb98b 100644
--- a/tests/test_pe.nf.test.snap
+++ b/tests/test_pe.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Bcl2Fastq_pe": {
         "content": [
-            7,
+            9,
             {
                 "BCL2FASTQ": {
                     "bcl2fastq": "2.20.0.422"
@@ -259,7 +259,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
                 "samplesheet",
-                "samplesheet/samplesheet.csv"
+                "samplesheet/atacseq_samplesheet.csv",
+                "samplesheet/rnaseq_samplesheet.csv",
+                "samplesheet/taxprofiler_samplesheet.csv"
             ],
             [
                 "PE_Sample.lane1_no_adapters.csv:md5,c31cca10b3a1aed8ec68daf779217d91",
@@ -320,8 +322,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-15T14:42:45.369275"
+        "timestamp": "2024-10-18T00:32:00.49132579"
     }
-}
+}
\ No newline at end of file
diff --git a/workflows/demultiplex.nf b/workflows/demultiplex.nf
index 7595afd1..bc960b7b 100644
--- a/workflows/demultiplex.nf
+++ b/workflows/demultiplex.nf
@@ -8,14 +8,16 @@
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
 
-include { BCL_DEMULTIPLEX           } from '../subworkflows/nf-core/bcl_demultiplex/main'
-include { FASTQ_CONTAM_SEQTK_KRAKEN } from '../subworkflows/nf-core/fastq_contam_seqtk_kraken/main'
-include { BASES_DEMULTIPLEX         } from '../subworkflows/local/bases_demultiplex/main'
-include { FQTK_DEMULTIPLEX          } from '../subworkflows/local/fqtk_demultiplex/main'
-include { MKFASTQ_DEMULTIPLEX       } from '../subworkflows/local/mkfastq_demultiplex/main'
-include { SINGULAR_DEMULTIPLEX      } from '../subworkflows/local/singular_demultiplex/main'
-include { RUNDIR_CHECKQC            } from '../subworkflows/local/rundir_checkqc/main'
-include { FASTQ_TO_SAMPLESHEET      } from '../modules/local/fastq_to_samplesheet/main'
+include { BCL_DEMULTIPLEX                                               } from '../subworkflows/nf-core/bcl_demultiplex/main'
+include { FASTQ_CONTAM_SEQTK_KRAKEN                                     } from '../subworkflows/nf-core/fastq_contam_seqtk_kraken/main'
+include { BASES_DEMULTIPLEX                                             } from '../subworkflows/local/bases_demultiplex/main'
+include { FQTK_DEMULTIPLEX                                              } from '../subworkflows/local/fqtk_demultiplex/main'
+include { MKFASTQ_DEMULTIPLEX                                           } from '../subworkflows/local/mkfastq_demultiplex/main'
+include { SINGULAR_DEMULTIPLEX                                          } from '../subworkflows/local/singular_demultiplex/main'
+include { RUNDIR_CHECKQC                                                } from '../subworkflows/local/rundir_checkqc/main'
+include { FASTQ_TO_SAMPLESHEET as FASTQ_TO_SAMPLESHEET_RNASEQ           } from '../modules/local/fastq_to_samplesheet/main'
+include { FASTQ_TO_SAMPLESHEET as FASTQ_TO_SAMPLESHEET_ATACSEQ          } from '../modules/local/fastq_to_samplesheet/main'
+include { FASTQ_TO_SAMPLESHEET as FASTQ_TO_SAMPLESHEET_TAXPROFILER      } from '../modules/local/fastq_to_samplesheet/main'
 
 //
 // MODULE: Installed directly from nf-core/modules
@@ -58,7 +60,7 @@ workflow DEMULTIPLEX {
     skip_tools          = params.skip_tools ? params.skip_tools.split(',') : []  // list: [falco, fastp, multiqc]
     sample_size         = params.sample_size                                     // int
     kraken_db           = params.kraken_db                                       // path
-    downstream_pipeline = params.downstream_pipeline                             // string: rnaseq, atacseq, taxprofiler
+    strandedness        = params.strandedness                                    // string: auto, reverse, forward, unstranded
 
     // Channel inputs
     ch_versions         = Channel.empty()
@@ -280,13 +282,31 @@ workflow DEMULTIPLEX {
     }
 
     // Module: FASTQ to samplesheet
-    FASTQ_TO_SAMPLESHEET(ch_meta_fastq, downstream_pipeline, 'auto')
+    ch_meta_fastq_rnaseq = ch_meta_fastq
+    FASTQ_TO_SAMPLESHEET_RNASEQ(ch_meta_fastq_rnaseq, "rnaseq", strandedness)
+    FASTQ_TO_SAMPLESHEET_RNASEQ.out.samplesheet
+            .map { it[1] }
+            .collectFile(name:'tmp_rnaseq_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName })
+            .map { it.text.tokenize('\n').join('\n') }
+            .collectFile(name:'rnaseq_samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
+            .set { ch_samplesheet }
+
+    ch_meta_fastq_atacseq = ch_meta_fastq
+    FASTQ_TO_SAMPLESHEET_ATACSEQ(ch_meta_fastq_atacseq, "atacseq", strandedness)
+    FASTQ_TO_SAMPLESHEET_ATACSEQ.out.samplesheet
+            .map { it[1] }
+            .collectFile(name:'tmp_atac_seq_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName })
+            .map { it.text.tokenize('\n').join('\n') }
+            .collectFile(name:'atacseq_samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
+            .set { ch_samplesheet }
 
-    FASTQ_TO_SAMPLESHEET.out.samplesheet
+    ch_meta_fastq_taxprofiler = ch_meta_fastq
+    FASTQ_TO_SAMPLESHEET_TAXPROFILER(ch_meta_fastq_taxprofiler, "taxprofiler", strandedness)
+    FASTQ_TO_SAMPLESHEET_TAXPROFILER.out.samplesheet
             .map { it[1] }
-            .collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName })
+            .collectFile(name:'tmp_taxprofiler_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName })
             .map { it.text.tokenize('\n').join('\n') }
-            .collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
+            .collectFile(name:'taxprofiler_samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
             .set { ch_samplesheet }
 
     //