feat: validate read structures with the nf-fgbio plugin

Author: nh13

nextflow.config

@@ -272,8 +272,10 @@ manifest {
 
 // Nextflow plugins
 // nf-schema: validation of pipeline parameters and creation of an input channel from a sample sheet
+// nf-fgbio: validation of read structure(s) passed as parameters
 plugins {
     id 'nf-schema@2.1.1'
+    id 'nf-fgbio@1.0.0'
 }
 
 validation {

subworkflows/local/utils_nfcore_fastquorum_pipeline/main.nf

@@ -11,6 +11,7 @@
 include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap } from 'plugin/nf-schema'
 include { samplesheetToList } from 'plugin/nf-schema'
+include { readStructure } from 'plugin/nf-fgbio'
 include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
@@ -177,6 +178,27 @@ def validateInputSamplesheetRow(row) {
     else if (num_segments > num_fastqs) {
         error("Please check input samplesheet -> Too many read structures (${num_segments}) for ${num_fastqs} FASTQs for ${meta.id}")
     }
+    
+    // Validate the read structure
+    meta.read_structure.tokenize(" ").each { rs->
+        // If parsing the read structure fails, then a java.lang.reflect.InvocationTargetException will be thrown, with
+        // the cause containing the exception produced by fgbio.
+        try {
+            readStructure(rs)
+        } catch (java.lang.reflect.InvocationTargetException ex) {
+            def message = """
+                |Please check input samplesheet -> Read structure`${rs}` invalid
+                |
+                |   ${ex.getCause().getMessage()}
+                |
+                |   For more information on read structures, visit: https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
+                |
+                |   Validate your read structures here: https://fulcrumgenomics.github.io/fgbio/validate-read-structure.html
+                |""".stripMargin()
+            error(message)
+            throw ex
+        }
+    }
 
     // NB: the collect here doesn't care which FASTQ list is empty
     return [row[0], row[1], row[2].findAll { it -> it.size() > 0 }]