Get rid of meta map from bbmap/index (#700)

Got rid of meta map from bbmap/index

modules/bbmap/index/main.nf

@@ -9,7 +9,7 @@ process BBMAP_INDEX {
     label 'process_long'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
     conda (params.enable_conda ? "bioconda::bbmap=38.92" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -19,10 +19,10 @@ process BBMAP_INDEX {
     }
 
     input:
-    tuple val(meta), path(fasta)
+    path fasta
 
     output:
-    tuple val(meta), path('ref')  , emit: index
+    path 'ref'                    , emit: index
     path "*.version.txt"          , emit: version
 
     script:

modules/bbmap/index/meta.yml

@@ -14,22 +14,12 @@ tools:
       licence: ['UC-LBL license (see package)']
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing optional parameters to bbmap.sh
-        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: fasta
       description: fasta formatted file with nucleotide sequences
       pattern: "*.{fna,fa,fasta}"
 
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - version:
       type: file
       description: File containing software version

tests/modules/bbmap/index/main.nf

@@ -6,8 +6,7 @@ include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams
 
 workflow test_bbmap_index {
     
-    input = [ [ id:'test' ], // meta map
+    input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-              file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
 
     BBMAP_INDEX ( input )
 }

tests/modules/bbmap/index/test.yml

@@ -7,6 +7,5 @@
     - bbmap/index
   files:
     - path: output/bbmap/ref/genome/1/chr1.chrom.gz
-      md5sum: fc20702f3378836f06d4104b9cd88918
     - path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
       md5sum: 9f0d9a7413c1d2c16cc24555b2381163