Add meta information to samtools/faidx (#1114)

* add meta to samtools/faidx

modules/samtools/faidx/main.nf

@@ -8,11 +8,11 @@ process SAMTOOLS_FAIDX {
         'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path "*.fai"       , emit: fai
-    path "versions.yml", emit: versions
+    tuple val(meta), path ("*.fai") , emit: fai
+    path "versions.yml"             , emit: versions
 
     script:
     def args = task.ext.args ?: ''

modules/samtools/faidx/meta.yml

@@ -14,11 +14,21 @@ tools:
         doi: 10.1093/bioinformatics/btp352
         licence: ['MIT']
 input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
     - fasta:
         type: file
         description: FASTA file
         pattern: "*.{fa,fasta}"
 output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
     - fai:
         type: file
         description: FASTA index file

tests/modules/samtools/faidx/main.nf

@@ -5,7 +5,9 @@ nextflow.enable.dsl = 2
 include { SAMTOOLS_FAIDX } from '../../../../modules/samtools/faidx/main.nf'
 
 workflow test_samtools_faidx {
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    SAMTOOLS_FAIDX ( fasta  )
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    SAMTOOLS_FAIDX ( input )
 }

tests/modules/samtools/faidx/test.yml

@@ -1,8 +1,10 @@
-- name: samtools faidx test workflow
-  command: nextflow run ./tests/modules/samtools/faidx -entry test_samtools_faidx -c ./tests/config/nextflow.config -c ./tests/modules/samtools/faidx/nextflow.config
+- name: samtools faidx test_samtools_faidx
+  command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools/faidx
   files:
     - path: output/samtools/genome.fasta.fai
       md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
+    - path: output/samtools/versions.yml
+      md5sum: d56671a7c8f8058944d3d536c3058f7f