Fix untar for centrifuge (#1472)

modules/centrifuge/main.nf

@@ -10,6 +10,7 @@ process CENTRIFUGE {
     input:
     tuple val(meta), path(reads)
     path db
+    val db_name
     val save_unaligned
     val save_aligned
     val sam_format
@@ -42,9 +43,8 @@ process CENTRIFUGE {
     }
     def sam_output = sam_format ? "--out-fmt 'sam'" : ''
     """
-    tar -xf $db
     centrifuge \\
-        -x $db_name \\
+        -x ${db}/${db_name} \\
         -p $task.cpus \\
         $paired \\
         --report-file ${prefix}.report.txt \\

modules/centrifuge/meta.yml

@@ -27,6 +27,9 @@ input:
       type: directory
       description: Centrifuge database in .tar.gz format
       pattern: "*.tar.gz"
+  - db_name:
+      type: string
+      description: Centrifuge database filenames without the suffix ".cf"
   - save_unaligned:
       type: value
       description: If true unmapped fastq files are saved

tests/modules/centrifuge/main.nf

@@ -2,18 +2,21 @@
 
 nextflow.enable.dsl = 2
 
+include { UNTAR      } from '../../../modules/untar/main.nf'
 include { CENTRIFUGE } from '../../../modules/centrifuge/main.nf'
 
 workflow test_centrifuge_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    db   =  file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
+    db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+    db_name = "minigut_cf"
     save_unaligned = true
     save_aligned = false
     sam_format = false
 
-    CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
+    UNTAR ( db )
+    CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] },db_name, save_unaligned, save_aligned, sam_format )
 
 }
 
@@ -22,12 +25,14 @@ workflow test_centrifuge_paired_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-     db   =  file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
+     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+     db_name = "minigut_cf"
      save_unaligned = true
      save_aligned = false
      sam_format = false
 
-    CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
+    UNTAR ( db )
+    CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, db_name, save_unaligned, save_aligned, sam_format )
 
 
 }