Added support for meta in bwamem2/index (#1921)

* Added support for meta in bwamem2/index

* Added missing description of the input meta map (fasta file)

* Made bwamem2/mem aware of the meta map the index carries

* The output meta map needs to be same as the input bam file

Don't merge it with the index's

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/bwamem2/index/main.nf

@@ -8,11 +8,11 @@ process BWAMEM2_INDEX {
         'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path "bwamem2"      , emit: index
+    tuple val(meta), path("bwamem2"), emit: index
-    path "versions.yml" , emit: versions
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/bwamem2/index/meta.yml

@@ -14,10 +14,20 @@ tools:
       documentation: https://github.com/bwa-mem2/bwa-mem2#usage
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Input genome fasta file
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - index:
       type: file
       description: BWA genome index files

modules/bwamem2/mem/main.nf

@@ -9,7 +9,7 @@ process BWAMEM2_MEM {
 
     input:
     tuple val(meta), path(reads)
-    path  index
+    tuple val(meta2), path(index)
     val   sort_bam
 
     output:

modules/bwamem2/mem/meta.yml

@@ -37,6 +37,11 @@ input:
       description: use samtools sort (true) or samtools view (false)
       pattern: "true or false"
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
       description: Output BAM file containing read alignments

tests/modules/bwamem2/index/main.nf

@@ -7,5 +7,5 @@ include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
 workflow test_bwamem2_index {
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BWAMEM2_INDEX ( fasta )
+    BWAMEM2_INDEX ( [ [id:'test'], fasta] )
 }

tests/modules/bwamem2/mem/main.nf

@@ -17,7 +17,7 @@ workflow test_bwamem2_mem_single_end {
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BWAMEM2_INDEX ( fasta )
+    BWAMEM2_INDEX ( [ [:], fasta ] )
     BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
 }
 
@@ -33,7 +33,7 @@ workflow test_bwamem2_mem_single_end_sort {
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BWAMEM2_INDEX ( fasta )
+    BWAMEM2_INDEX ( [ [:], fasta ] )
     BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
 }
 
@@ -51,7 +51,7 @@ workflow test_bwamem2_mem_paired_end {
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BWAMEM2_INDEX ( fasta )
+    BWAMEM2_INDEX ( [ [:], fasta ] )
     BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
 }
 
@@ -68,6 +68,6 @@ workflow test_bwamem2_mem_paired_end_sort {
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BWAMEM2_INDEX ( fasta )
+    BWAMEM2_INDEX ( [ [:], fasta ] )
     BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
 }