nf-core · aidaanva · Mar 7, 2025 · Mar 28, 2025 · Apr 4, 2025 · Apr 4, 2025
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -73,6 +73,18 @@
                 "type": "string",
                 "meta": ["bam_reference_id"],
                 "errorMessage": "A BAM reference ID (corresponding to what is supplied to `--fasta`) must always be provided when providing a BAM file."
+            },
+            "vcf": {
+                "type": "string",
+                "format": "file-path",
+                "pattern": "^\\S+\\.vcf.gz$",
+                "exists": true,
+                "errorMessage": "VCFs files cannot contain any spaces and must have extension '.vcf.gz' and be gzip zipped."
+            },
+            "vcf_reference_id": {
+                "type": "string",
+                "meta": ["vcf_reference_id"],
+                "errorMessage": "A VCF reference ID (corresponding to what is supplied to `--fasta`) must always be provided when providing a VCF file."
             }
         },
         "required": [
@@ -90,18 +102,24 @@
             },
             {
                 "required": ["bam"]
+            },
+            {
+                "required": ["vcf"]
             }
         ],
         "dependentRequired": {
             "r2": ["r1"],
             "bam": ["bam_reference_id"],
-            "bam_reference_id": ["bam"]
+            "bam_reference_id": ["bam"],
+            "vcf" : ["vcf_reference_id"],
+            "vcf_reference_id" : ["vcf"]
         }
     },
     "allOf": [
         { "uniqueEntries": ["lane", "library_id"] },
         { "uniqueEntries": "r1" },
         { "uniqueEntries": "r2" },
-        { "uniqueEntries": "bam" }
+        { "uniqueEntries": "bam" },
+        { "uniqueEntries": "vcf" }
     ]
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -1752,4 +1752,35 @@ process {
             ]
         ]
     }
+
+    withName: UG_BGZIP {
+        tag = { "${meta.reference}|${meta.sample_id}" }
+        ext.args = "-d"
+    }
+
+    withName: REF_MVA_GUNZIP {
+        tag = { "${meta.reference}" }
+        ext.args = "-d"
+    }
+
+    withName: MULTIVCFANALYZER {
+        tag = { "${meta.reference}" }
+        ext.prefix = { "multivcfanalyzer_${meta.reference}" }
+        publishDir = [
+            [
+                // data
+                path: { "${params.outdir}/consensus_sequence/data/" },
+                mode: params.publish_dir_mode,
+                enabled: true,
+                pattern: '*.fastq.gz'
+            ],
+            [
+                // stats
+                path: { "${params.outdir}/consensus_sequence/stats/" },
+                mode: params.publish_dir_mode,
+                enabled: true,
+                pattern: '*.{txt,tsv}'
+            ]
+        ]
+    }
 }
diff --git a/main.nf b/main.nf
@@ -45,6 +45,7 @@ workflow NFCORE_EAGER {
     take:
     samplesheet_fastqs // channel: samplesheet read in from --input
     samplesheet_bams
+    samplesheet_vcfs
 
     main:
 
@@ -53,7 +54,8 @@ workflow NFCORE_EAGER {
     //
     EAGER (
         samplesheet_fastqs,
-        samplesheet_bams
+        samplesheet_bams,
+        samplesheet_vcfs
     )
     emit:
     multiqc_report = EAGER.out.multiqc_report // channel: /path/to/multiqc_report.html
@@ -85,6 +87,7 @@ workflow {
     NFCORE_EAGER (
         PIPELINE_INITIALISATION.out.samplesheet_fastqs,
         PIPELINE_INITIALISATION.out.samplesheet_bams,
+        PIPELINE_INITIALISATION.out.samplesheet_vcfs
     )
     //
     // SUBWORKFLOW: Run completion tasks