From 734d0db6079a4aa43b6509b207e5d6feb35d4838 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Wed, 27 Jul 2022 14:24:06 +0200
Subject: [PATCH] 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        |  4 ++--
 modules/centrifuge/kreport/meta.yml       |  4 ++--
 tests/modules/centrifuge/kreport/test.yml | 18 ++++++++----------
 3 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/modules/centrifuge/kreport/main.nf b/modules/centrifuge/kreport/main.nf
index 124cbdba..381ddd6c 100644
--- a/modules/centrifuge/kreport/main.nf
+++ b/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}":
diff --git a/modules/centrifuge/kreport/meta.yml b/modules/centrifuge/kreport/meta.yml
index fbcae24f..822a280e 100644
--- a/modules/centrifuge/kreport/meta.yml
+++ b/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:
diff --git a/tests/modules/centrifuge/kreport/test.yml b/tests/modules/centrifuge/kreport/test.yml
index 167cb0dc..ab614c53 100644
--- a/tests/modules/centrifuge/kreport/test.yml
+++ b/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