diff --git a/.gitignore b/.gitignore
index cc2b1a7..5516a06 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ testing*
 *.pyc
 null/
 .lineage/
+.nf-test*
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60dad40..36d6f40 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@ Initial release of nf-core/datasync, created with the [nf-core](https://nf-co.re
 
 ### `Added`
 
+- [[#31](https://github.com/nf-core/datasync/pull/31)] - Compute checksum for each input file ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila)).
+
 ### `Fixed`
 
 ### `Dependencies`
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index 5f653ab..55cd8f9 100644
--- a/assets/samplesheet.csv
+++ b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,input
+human_grch38_sequence,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/
+test_fastq,https://github.com/nf-core/test-datasets/raw/71ac9e72555f901d2864ccb27d534933411e3ed4/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 248b66e..4afb584 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -13,21 +13,12 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
-            "fastq_1": {
+            "input": {
                 "type": "string",
-                "format": "file-path",
-                "exists": true,
-                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "type": "string",
-                "format": "file-path",
-                "exists": true,
-                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "^\\S+$",
+                "errorMessage": "Input path must be provided and cannot contain spaces"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "input"]
     }
 }
diff --git a/conf/test.config b/conf/test.config
index 7b7af9e..3f62cb0 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -25,6 +25,6 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references
+    input = "${projectDir}/assets/samplesheet.csv"
     genome = 'R64-1-1'
 }
diff --git a/modules.json b/modules.json
index 578acbb..13a67eb 100644
--- a/modules.json
+++ b/modules.json
@@ -10,10 +10,20 @@
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
+                    "md5sum": {
+                        "branch": "master",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
+                    },
+                    "shasum": {
+                        "branch": "master",
+                        "git_sha": "ef2ee0358c7d03231834aeac816991aeb20debd7",
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/modules/nf-core/md5sum/environment.yml b/modules/nf-core/md5sum/environment.yml
new file mode 100644
index 0000000..9b926b1
--- /dev/null
+++ b/modules/nf-core/md5sum/environment.yml
@@ -0,0 +1,12 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/nf-core/md5sum/main.nf b/modules/nf-core/md5sum/main.nf
new file mode 100644
index 0000000..7dafd75
--- /dev/null
+++ b/modules/nf-core/md5sum/main.nf
@@ -0,0 +1,55 @@
+process MD5SUM {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
+
+    input:
+    tuple val(meta), path(files)
+    val as_separate_files
+
+    output:
+    tuple val(meta), path("*.md5"), emit: checksum
+    tuple val("${task.process}"), val('md5sum'), eval("md5sum --version | sed '1!d; s/.* //'"), topic: versions, emit: versions_md5sum
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // will only use when as_separate_files = false
+    if (as_separate_files) {
+        """
+        find -L * -maxdepth 0 -type f \\
+            ! -name '*.md5' \\
+            -exec sh -c 'md5sum ${args} "\$1" > "\$1.md5"' _ "{}" \\;
+        """
+    }
+    else {
+        """
+        find -L * -type f \\
+            ! -name '*.md5' \\
+            -exec md5sum ${args} "{}" + \\
+            > ${prefix}.md5
+        """
+    }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (as_separate_files) {
+        """
+        find -L * -type f \\
+            ! -name '*.md5' \\
+            -exec sh -c 'touch "\$1.md5"' _ "{}" \\;
+        """
+    }
+    else {
+        """
+        touch ${prefix}.md5
+        """
+    }
+}
diff --git a/modules/nf-core/md5sum/meta.yml b/modules/nf-core/md5sum/meta.yml
new file mode 100644
index 0000000..71066a8
--- /dev/null
+++ b/modules/nf-core/md5sum/meta.yml
@@ -0,0 +1,68 @@
+name: "md5sum"
+description: Create MD5 (128-bit) checksums
+keywords:
+  - checksum
+  - MD5
+  - 128 bit
+tools:
+  - "md5sum":
+      description: Create MD5 (128-bit) checksums for each file
+      homepage: "https://www.gnu.org"
+      documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html"
+      licence:
+        - "GPL-3.0-or-later"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - files:
+        type: file
+        description: Any number of files. One md5sum file will be generated for
+          each.
+        pattern: "*.*"
+        ontologies: []
+  - as_separate_files:
+      type: boolean
+      description: |
+        If true, each file will have its own md5sum file. If false, all files will be
+        checksummed into a single md5sum file.
+output:
+  checksum:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.md5":
+          type: file
+          description: File containing checksum
+          pattern: "*.md5"
+          ontologies: []
+  versions_md5sum:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - md5sum:
+          type: string
+          description: The name of the tool
+      - md5sum --version | sed '1!d; s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - md5sum:
+          type: string
+          description: The name of the tool
+      - md5sum --version | sed '1!d; s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@matthdsm"
+maintainers:
+  - "@matthdsm"
diff --git a/modules/nf-core/md5sum/tests/main.nf.test b/modules/nf-core/md5sum/tests/main.nf.test
new file mode 100644
index 0000000..a6f7cf8
--- /dev/null
+++ b/modules/nf-core/md5sum/tests/main.nf.test
@@ -0,0 +1,180 @@
+nextflow_process {
+
+    name "Test Process MD5SUM"
+    script "../main.nf"
+    process "MD5SUM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "md5sum"
+
+    test("md5sum on hello.txt") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'hello' ],
+                    [ file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) ]
+                ]
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+    test("md5sum on hello.txt (BSD-style)") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'hello' ],
+                    [ file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) ]
+                ]
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+    test("md5sum on hello.txt - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'hello' ],
+                    [ file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) ]
+                ]
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+    test("md5sum on paired fastq, combined") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+    test("md5sum on paired fastq, combined - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+
+    test("md5sum on paired fastq, separate") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+    test("md5sum on paired fastq, separate - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                { assert process.success }
+                { assert snapshot(process.out).match() }
+            }
+        }
+    }
+
+}
diff --git a/modules/nf-core/md5sum/tests/main.nf.test.snap b/modules/nf-core/md5sum/tests/main.nf.test.snap
new file mode 100644
index 0000000..bf78c29
--- /dev/null
+++ b/modules/nf-core/md5sum/tests/main.nf.test.snap
@@ -0,0 +1,301 @@
+{
+    "md5sum on paired fastq, separate - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_1.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_2.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_1.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_2.fastq.gz.md5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:31:17.339668",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "md5sum on paired fastq, separate": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_1.fastq.gz.md5:md5,63a3f187d06ae5cffe77fcd39bbdd63a",
+                            "test_2.fastq.gz.md5:md5,055dc46636836dbd1d9ede2e6ce8cd4e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_1.fastq.gz.md5:md5,63a3f187d06ae5cffe77fcd39bbdd63a",
+                            "test_2.fastq.gz.md5:md5,055dc46636836dbd1d9ede2e6ce8cd4e"
+                        ]
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:31:11.522274",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "md5sum on hello.txt - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        "hello.txt.md5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        "hello.txt.md5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:30:52.301881",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "md5sum on hello.txt": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        "hello.txt.md5:md5,5c18e1db5460fb32fed66966483165fd"
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        "hello.txt.md5:md5,5c18e1db5460fb32fed66966483165fd"
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:30:41.089186",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "md5sum on paired fastq, combined": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.md5:md5,dfb98e45cbb77a9a63ae7029aee38bd1"
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.md5:md5,dfb98e45cbb77a9a63ae7029aee38bd1"
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:30:58.611754",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "md5sum on paired fastq, combined - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.md5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.md5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:31:06.064053",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "md5sum on hello.txt (BSD-style)": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        "hello.txt.md5:md5,152a03f5dc7aa8db6612f63154ecbca2"
+                    ]
+                ],
+                "1": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ],
+                "checksum": [
+                    [
+                        {
+                            "id": "hello"
+                        },
+                        "hello.txt.md5:md5,152a03f5dc7aa8db6612f63154ecbca2"
+                    ]
+                ],
+                "versions_md5sum": [
+                    [
+                        "MD5SUM",
+                        "md5sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-18T14:30:46.389675",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/md5sum/tests/nextflow.config b/modules/nf-core/md5sum/tests/nextflow.config
new file mode 100644
index 0000000..4acada5
--- /dev/null
+++ b/modules/nf-core/md5sum/tests/nextflow.config
@@ -0,0 +1,2 @@
+
+process.ext.args = '--tag'
diff --git a/modules/nf-core/shasum/environment.yml b/modules/nf-core/shasum/environment.yml
new file mode 100644
index 0000000..9b926b1
--- /dev/null
+++ b/modules/nf-core/shasum/environment.yml
@@ -0,0 +1,12 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/nf-core/shasum/main.nf b/modules/nf-core/shasum/main.nf
new file mode 100644
index 0000000..2fa689d
--- /dev/null
+++ b/modules/nf-core/shasum/main.nf
@@ -0,0 +1,33 @@
+process SHASUM {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), path("*.sha256"), emit: checksum
+    tuple val("${task.process}"), val('sha256sum'), eval("sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'"), emit: versions_sha256sum, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    sha256sum \\
+        ${args} \\
+        ${file} \\
+        > ${file}.sha256
+    """
+
+    stub:
+    """
+    touch ${file}.sha256
+    """
+}
diff --git a/modules/nf-core/shasum/meta.yml b/modules/nf-core/shasum/meta.yml
new file mode 100644
index 0000000..327a4f0
--- /dev/null
+++ b/modules/nf-core/shasum/meta.yml
@@ -0,0 +1,62 @@
+name: "shasum"
+description: Print SHA256 (256-bit) checksums.
+keywords:
+  - checksum
+  - sha256
+  - 256 bit
+tools:
+  - "md5sum":
+      description: Create an SHA256 (256-bit) checksum.
+      homepage: "https://www.gnu.org"
+      documentation: "https://linux.die.net/man/1/shasum"
+      licence:
+        - "GPLv3+"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - file:
+        type: file
+        description: Any file
+        pattern: "*.*"
+        ontologies: []
+output:
+  checksum:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.sha256":
+          type: file
+          description: File containing checksum
+          pattern: "*.sha256"
+          ontologies: []
+  versions_sha256sum:
+    - - ${task.process}:
+          type: string
+          description: Process name
+      - sha256sum:
+          type: string
+          description: Tool name
+      - "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'":
+          type: eval
+          description: Software version
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: Process name
+      - sha256sum:
+          type: string
+          description: Tool name
+      - "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'":
+          type: eval
+          description: Software version
+authors:
+  - "@matthdsm"
+maintainers:
+  - "@matthdsm"
diff --git a/modules/nf-core/shasum/tests/main.nf.test b/modules/nf-core/shasum/tests/main.nf.test
new file mode 100644
index 0000000..02d2ac0
--- /dev/null
+++ b/modules/nf-core/shasum/tests/main.nf.test
@@ -0,0 +1,58 @@
+
+nextflow_process {
+
+    name "Test Process SHASUM"
+    script "../main.nf"
+    process "SHASUM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shasum"
+
+    test("test-shasum") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("test-shasum - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/shasum/tests/main.nf.test.snap b/modules/nf-core/shasum/tests/main.nf.test.snap
new file mode 100644
index 0000000..a86583b
--- /dev/null
+++ b/modules/nf-core/shasum/tests/main.nf.test.snap
@@ -0,0 +1,56 @@
+{
+    "test-shasum": {
+        "content": [
+            {
+                "checksum": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.bam.sha256:md5,138a19e100f09fc975ea1b717da9b6dd"
+                    ]
+                ],
+                "versions_sha256sum": [
+                    [
+                        "SHASUM",
+                        "sha256sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-03T20:43:40.688253838",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "24.10.4"
+        }
+    },
+    "test-shasum - stub": {
+        "content": [
+            {
+                "checksum": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.bam.sha256:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_sha256sum": [
+                    [
+                        "SHASUM",
+                        "sha256sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-03T20:43:46.125782074",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "24.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf
index e9e92f3..db1f6d4 100644
--- a/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_datasync_pipeline/main.nf
@@ -110,21 +110,15 @@ workflow PIPELINE_INITIALISATION {
     channel
         .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
         .map {
-            meta, fastq_1, fastq_2 ->
-                if (!fastq_2) {
-                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
+            meta, input_path ->
+                def target = file(input_path)
+                if (target.isDirectory()) {
+                    def all_files = files("${input_path}/**", type: 'file')
+                    [meta, all_files]
                 } else {
-                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+                    [meta, [target]]
                 }
         }
-        .groupTuple()
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
-        }
-        .map {
-            meta, fastqs ->
-                return [ meta, fastqs.flatten() ]
-        }
         .set { ch_samplesheet }
 
     emit:
@@ -189,20 +183,6 @@ def validateInputParameters() {
     genomeExistsError()
 }
 
-//
-// Validate channels from input samplesheet
-//
-def validateInputSamplesheet(input) {
-    def (metas, fastqs) = input[1..2]
-
-    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
-    if (!endedness_ok) {
-        error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
-    }
-
-    return [ metas[0], fastqs ]
-}
 //
 // Get attribute from genome config file e.g. fasta
 //
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 466aab7..f48ad94 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -2,11 +2,20 @@
     "-profile test": {
         "content": [
             {
+                "MD5SUM": {
+                    "md5sum": 9.5
+                },
+                "SHASUM": {
+                    "sha256sum": 9.5
+                },
                 "Workflow": {
                     "nf-core/datasync": "v1.0dev"
                 }
             },
             [
+                "md5sum",
+                "md5sum/human_grch38_sequence.md5",
+                "md5sum/test_fastq.md5",
                 "multiqc",
                 "multiqc/multiqc_data",
                 "multiqc/multiqc_data/llms-full.txt",
@@ -18,16 +27,33 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_datasync_software_mqc_versions.yml"
+                "pipeline_info/nf_core_datasync_software_mqc_versions.yml",
+                "shasum",
+                "shasum/GenomeSize.xml.old.sha256",
+                "shasum/GenomeSize.xml.sha256",
+                "shasum/genome.dict.old.sha256",
+                "shasum/genome.dict.sha256",
+                "shasum/genome.fa.fai.sha256",
+                "shasum/genome.fa.sha256",
+                "shasum/test2_1.fastq.gz.sha256"
             ],
             [
-                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+                "human_grch38_sequence.md5:md5,0547c2f89caeb0e8e7d67da583e09d90",
+                "test_fastq.md5:md5,145df327e566f16b545fbca236f9bb62",
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "GenomeSize.xml.old.sha256:md5,068e91cdcc084710caf61a0859ac2be9",
+                "GenomeSize.xml.sha256:md5,e7a175f04cab11ce0a245133d70de9fb",
+                "genome.dict.old.sha256:md5,77492c77f911887b269de347e157d4ca",
+                "genome.dict.sha256:md5,0021eaba625d4dc9fcec55eb7384426e",
+                "genome.fa.fai.sha256:md5,99f227079c0fd354f272c0046482ff1a",
+                "genome.fa.sha256:md5,9bdb272c4b51342a0f139fbc14d0a57e",
+                "test2_1.fastq.gz.sha256:md5,3407e7acd19b8bb0f0b731a046e7943f"
             ]
         ],
+        "timestamp": "2026-06-16T18:04:56.374326627",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "26.04.3"
-        },
-        "timestamp": "2026-06-12T19:01:37.766797147"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
     }
 }
\ No newline at end of file
diff --git a/workflows/datasync.nf b/workflows/datasync.nf
index ee20e12..6e6c910 100644
--- a/workflows/datasync.nf
+++ b/workflows/datasync.nf
@@ -3,7 +3,9 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
+include { MD5SUM                 } from '../modules/nf-core/md5sum/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+include { SHASUM                 } from '../modules/nf-core/shasum/main'
 include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -29,6 +31,15 @@ workflow DATASYNC {
     ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
 
+    MD5SUM(
+        ch_samplesheet,
+        false
+    )
+
+    SHASUM(
+        ch_samplesheet.transpose()
+    )
+
     //
     // Collate and save software versions
     //