antoniasaracco · Jun 23, 2026 · Jun 18, 2026 · Jun 18, 2026 · Jun 18, 2026 · Jun 18, 2026
diff --git a/assets/samplesheet_full.csv b/assets/samplesheet_full.csv
@@ -0,0 +1,2 @@
+sample,input,checksum_md5,checksum_sha
+demultiplex,s3://nf-core-awsmegatests/demultiplex/results-fbec8e442f0599f8b74876e62263af05b9a41d33/,checksum_md5.tsv,checksum_sha.tsv
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -17,6 +17,16 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Input path must be provided and cannot contain spaces"
+            },
+            "checksum_md5": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Checksum_md5 cannot contain spaces"
+            },
+            "checksum_sha": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Checksum_sha cannot contain spaces"
             }
         },
         "required": ["sample", "input"]

diff --git a/conf/modules.config b/conf/modules.config
@@ -18,10 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: FASTQC {
-        ext.args = '--quiet'
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,7 +17,7 @@ params {
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // 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_full_illumina_amplicon.csv'
+    input = params.pipelines_testdata_base_path + "test-data/samplesheet.csv"
 
     // Genome references
     genome = 'R64-1-1'

diff --git a/modules.json b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
-                        "installed_by": ["modules"]
-                    },
                     "md5sum": {
                         "branch": "master",
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
@@ -22,7 +17,7 @@
                     },
                     "shasum": {
                         "branch": "master",
-                        "git_sha": "ef2ee0358c7d03231834aeac816991aeb20debd7",
+                        "git_sha": "429d56ab5b5879549f71bf9905104f39d0c3bff4",
                         "installed_by": ["modules"]
                     }
                 }
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample,input,checksum_md5,checksum_sha
		demultiplex,s3://nf-core-awsmegatests/demultiplex/results-fbec8e442f0599f8b74876e62263af05b9a41d33/,checksum_md5.tsv,checksum_sha.tsv
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