Use samplesheet row in id

Co-authored-by: Matthias Zepper <[email protected]>

Author: Aratz

subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

@@ -82,19 +82,21 @@ workflow PIPELINE_INITIALISATION {
     //
     Channel
         .fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
+        .toList()
+        .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
         .map {
-            meta, fastq_1, fastq_2 ->
+            meta, fastq_1, fastq_2, idx ->
                 def tags = meta.tags ? meta.tags.tokenize(":") : []
-                def updated_meta = meta + [ id:meta.sample, tags:tags ]
+                def updated_meta = meta + [ id:"${meta.sample}_${idx}", tags:tags ]
                 if (!fastq_2) {
                     return [
-                        updated_meta.id + fastq_1.toString().replaceAll('/', '_'),
+                        updated_meta.id,
                         updated_meta + [ single_end:true ],
                         [ fastq_1 ]
                     ]
                 } else {
                     return [
-                        updated_meta.id + fastq_1.toString().replaceAll('/', '_') + '_' + fastq_2.toString().replaceAll('/', '_'),
+                        updated_meta.id,
                         updated_meta + [ single_end:false ],
                         [ fastq_1, fastq_2 ]
                     ]