From b8aaea7429e74cb23acff21b03ba3814d7905ed1 Mon Sep 17 00:00:00 2001
From: jvhagey <qpk9@cdc.gov>
Date: Tue, 24 May 2022 16:27:00 -0400
Subject: [PATCH] updating paths in test.yml

---
 modules/gamma/gamma/main.nf        |  2 +-
 modules/gamma/gamma/meta.yml       |  3 ++-
 tests/modules/gamma/gamma/main.nf  |  6 +++---
 tests/modules/gamma/gamma/test.yml | 20 ++++++++++----------
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/modules/gamma/gamma/main.nf b/modules/gamma/gamma/main.nf
index 51a5f6c8..fddced62 100644
--- a/modules/gamma/gamma/main.nf
+++ b/modules/gamma/gamma/main.nf
@@ -1,6 +1,6 @@
 def VERSION = '2.1' // Version information not provided by tool on CLI
 
-process GAMMA {
+process GAMMA_GAMMA {
     tag "$meta.id"
     label 'process_low'
 
diff --git a/modules/gamma/gamma/meta.yml b/modules/gamma/gamma/meta.yml
index 316b685b..d9e272e2 100644
--- a/modules/gamma/gamma/meta.yml
+++ b/modules/gamma/gamma/meta.yml
@@ -1,4 +1,4 @@
-name: "gamma"
+name: "gamma_gamma"
 description: Gene Allele Mutation Microbial Assessment
 keywords:
   - gamma
@@ -61,3 +61,4 @@ output:
 authors:
   - "@sateeshperi"
   - "@rastanton"
+  - "@jvhagey"
diff --git a/tests/modules/gamma/gamma/main.nf b/tests/modules/gamma/gamma/main.nf
index 070a3bf1..97e58be7 100644
--- a/tests/modules/gamma/gamma/main.nf
+++ b/tests/modules/gamma/gamma/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { GAMMA } from '../../../../modules/gamma/gamma/main.nf'
+include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf'
 
 workflow test_unzip {
 
@@ -13,7 +13,7 @@ workflow test_unzip {
 
     db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
 
-    GAMMA ( input, db )
+    GAMMA_GAMMA ( input, db )
 }
 
 workflow test_gamma {
@@ -25,5 +25,5 @@ workflow test_gamma {
 
     db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
 
-    GAMMA ( input, db )
+    GAMMA_GAMMA ( input, db )
 }
diff --git a/tests/modules/gamma/gamma/test.yml b/tests/modules/gamma/gamma/test.yml
index 308d890f..2c649105 100644
--- a/tests/modules/gamma/gamma/test.yml
+++ b/tests/modules/gamma/gamma/test.yml
@@ -4,14 +4,14 @@
     - gamma/gamma
     - gamma
   files:
-    - path: /tmp/tmppm1ybfln/gamma/test.fasta
+    - path: output/gamma/gamma/test.fasta
       md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
-    - path: /tmp/tmppm1ybfln/gamma/test.gamma
+    - path: output/gamma/gamma/test.gamma
       md5sum: 46165a89e10b7315d3a9b0aa6c561626
-    - path: /tmp/tmppm1ybfln/gamma/test.psl
+    - path: output/gamma/gamma/test.psl
       md5sum: f489ce4602ddbcb692d5781ee3fbf449
-    - path: /tmp/tmppm1ybfln/gamma/versions.yml
-      md5sum: ad23c3ec60663598543cbe8bc74bc4ab
+    - path: output/gamma/gamma/versions.yml
+      md5sum: 8baafec7b3b87f788f69e30d317c9722
 
 - name: gamma gamma test_gamma
   command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
@@ -19,11 +19,11 @@
     - gamma/gamma
     - gamma
   files:
-    - path: /tmp/tmpw3chm6da/gamma/test.fasta
+    - path: output/gamma/gamma/test.fasta
       md5sum: df37b48466181311e0a679f3c5878484
-    - path: /tmp/tmpw3chm6da/gamma/test.gamma
+    - path: output/gamma/gamma/test.gamma
       md5sum: 3256708fa517a65ed01d99e0e3c762ae
-    - path: /tmp/tmpw3chm6da/gamma/test.psl
+    - path: output/gamma/gamma/test.psl
       md5sum: 162a2757ed3b167ae1e0cdb24213f940
-    - path: /tmp/tmpw3chm6da/gamma/versions.yml
-      md5sum: 3fefb5b46c94993362243c5f9a472057
+    - path: output/gamma/gamma/versions.yml
+      md5sum: b75c2871d8cac2f8ac67c0fbd22babd6