bclconvert: Update Dockerfile (#1819)

* Update Dockerfile

* Output only top level InterOp files

* Update tag

Author: matthdsm

modules/bclconvert/Dockerfile

@@ -11,5 +11,7 @@ RUN apt-get update \
     && apt-get install -y \
     procps \
     && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+# Link hostname cmd to fix hardcoded path
+RUN ln -s /bin/hostname /usr/bin/hostname
 COPY bcl-convert /usr/local/bin/bcl-convert
 RUN chmod +x /usr/local/bin/bcl-convert

modules/bclconvert/main.nf

@@ -1,5 +1,5 @@
 process BCLCONVERT {
-    tag "$meta.id"
+    tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
     label 'process_high'
 
     if (params.enable_conda) {
@@ -17,7 +17,7 @@ process BCLCONVERT {
     tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz")       ,optional:true, emit: undetermined_idx
     tuple val(meta), path("Reports")                                    ,emit: reports
     tuple val(meta), path("Logs")                                       ,emit: logs
-    tuple val(meta), path("**.bin")                                     ,emit: interop
+    tuple val(meta), path("**/InterOp/*.bin")                           ,emit: interop
     path("versions.yml")                                                ,emit: versions
 
     when: