Merge pull request nf-core#638 from nf-core/fix_fastqc_samplenames

Fix fastqc samplenames in multiqc report

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)
 - Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
 - Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
 - Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)

assets/multiqc_config.yml

@@ -44,6 +44,6 @@ module_order:
 extra_fn_clean_exts:
   - "_sorted_md"
   - type: regex
-    pattern: "_T[0-9]"
+    pattern: "_LNUMBER[0-9]{1,}"
 
 disable_version_detection: true

subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf

@@ -97,7 +97,7 @@ workflow PIPELINE_INITIALISATION {
         }
         .combine( ch_input_counts )
         .map { lineno, meta, fastqs -> //append line number to sampleid
-            new_meta = meta + [id:meta.id+"_T"+lineno[fastqs]]
+            new_meta = meta + [id:meta.id+"_LNUMBER"+lineno[fastqs]]
             return [ new_meta, fastqs ]
         }
         .set { ch_samplesheet }