integrate review comments

nf-core · Oct 20, 2023 · 6e2abeb · 6e2abeb
1 parent 2cf99e1
commit 6e2abeb
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/subworkflows/local/map.nf b/subworkflows/local/map.nf
@@ -29,8 +29,7 @@ workflow MAP {
                                 .map{
                                     // create meta consistent with rest of workflow
                                     meta, bam ->
-                                    new_meta = meta.clone()
-                                    new_meta.reference = meta.id_index
+                                    new_meta = meta + [ reference: meta.id_index ]
                                 [ new_meta, bam ]
                                 }
 
@@ -41,10 +40,9 @@ workflow MAP {
                             .combine( index )
                             .multiMap {
                                 meta, reads, meta2, index ->
-                                    new_meta = meta.clone()
-                                    new_meta.reference = meta2.id
+                                    new_meta = meta + [ reference: meta2.id ]
                                     reads: [ new_meta, reads ]
-                                    index: [ meta2, index]
+                                    index: [ meta2, index ]
                             }
 
         BWA_MEM ( ch_input_for_mapping.reads, ch_input_for_mapping.index, true )
@@ -60,10 +58,9 @@ workflow MAP {
                             .combine( index )
                             .multiMap {
                                 meta, reads, meta2, index ->
-                                    new_meta = meta.clone()
-                                    new_meta.reference = meta2.id
+                                    new_meta = meta + [ reference: meta2.id ]
                                     reads: [ new_meta, reads ]
-                                    index: [ meta2, index]
+                                    index: [ meta2, index ]
                             }
 
         BOWTIE2_ALIGN ( ch_input_for_mapping.reads, ch_input_for_mapping.index, false, true )

diff --git a/workflows/eager.nf b/workflows/eager.nf
@@ -295,12 +295,14 @@ workflow EAGER {
                 bam:             [ meta, bam ]
                 snp_capture_bed: [ snp_capture_bed ]
             }
+
         QUALIMAP_BAMQC_WITHBED( ch_qualimap_input_with.bam, ch_qualimap_input_with.snp_capture_bed )
         ch_qualimap_input_without = ch_qualimap_input.nobed
             .map{
                 ignore_meta, meta, bam, meta2, snp_capture_bed ->
                 [ meta, bam ]
             }
+
         QUALIMAP_BAMQC_NOBED( ch_qualimap_input_without, [] )
         ch_qualimap_output = QUALIMAP_BAMQC_WITHBED.out.results.mix( QUALIMAP_BAMQC_NOBED.out.results )
         ch_versions = ch_versions.mix( QUALIMAP_BAMQC_NOBED.out.versions ).mix( QUALIMAP_BAMQC_WITHBED.out.versions )