Update module: Use report insted of results for centrifuge/kreport (#1929)

* Use report insted of results for kreport

* Update modules/centrifuge/kreport/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/centrifuge/kreport/main.nf

@@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
         'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
 
     input:
-    tuple val(meta), path(results)
+    tuple val(meta), path(report)
     path db
 
     output:
@@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
-    centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
+    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/centrifuge/kreport/meta.yml

@@ -15,9 +15,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - results:
+  - report:
       type: file
-      description: File containing the centrifuge classification results
+      description: File containing the centrifuge classification report
       pattern: "*.{txt}"
 
 output:

tests/modules/centrifuge/kreport/test.yml

@@ -1,21 +1,19 @@
 - name: centrifuge kreport test_centrifuge_kreport_single_end
-  command: nextflow run tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/centrifuge/kreport/nextflow.config
   tags:
-    - centrifuge
     - centrifuge/kreport
+    - centrifuge
   files:
+    - path: output/centrifuge/test.report.txt
+    - path: output/centrifuge/test.results.txt
     - path: output/centrifuge/test.txt
-      md5sum: af1a51fe57eb6d428350ff4a4bf759d4
-      contains: ["unclassified"]
-    - path: output/centrifuge/versions.yml
 
 - name: centrifuge kreport test_centrifuge_kreport_paired_end
-  command: nextflow run tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/centrifuge/kreport/nextflow.config
   tags:
-    - centrifuge
     - centrifuge/kreport
+    - centrifuge
   files:
+    - path: output/centrifuge/test.report.txt
+    - path: output/centrifuge/test.results.txt
     - path: output/centrifuge/test.txt
-      md5sum: af1a51fe57eb6d428350ff4a4bf759d4
-      contains: ["unclassified"]
-    - path: output/centrifuge/versions.yml